I read that in the Middle Ages, charging interest was banned entirely at the Church's behest. However these days the Church only condemns excessive rates of interest, and even charges interest itself. This change occurred before Vatican 2, so we can all agree it was done under a valid Pope and wasn't the work of freemason or Jєωιѕн infiltration, and I do not mean at all to imply it was done for nefarious reasons. But why was it done? I'm interested in the reasoning behind it.

We can all agree it was done under valid popes, but I do not agree it was not the work of freemason or Jєωιѕн infiltration.  Freemason and Jєωιѕн infiltrators can become pope, and I believe in the past they probably have been.  And, if it was not done for nefarious or impious reasons, it was certainly done out of ignorance, because since the very beginning when interest on loans(montes peitatis) took root in the church, it has been hotly debated, ugly, and riddled with abuse.   And, it has not waned one bit.  It has only been distracted from by other issues.    

Next, don't set yourself on understanding why it was done.  You will never receive that answer.  Simply study the matter and the facts, and base your opinions off of that.  Because, there is enough to discuss concerning usury without having to discuss why such and such a pope did this, and was this pope a valid pope based off of your findings.  Or perhaps do that, and you will come to find that the problems in the church go back long before vatican 2, and that sedevacantism indeed is not the answer.  Because, there has been constant papal corruption and negligence(one or both) for at least 700 years.  Yet, we still have a papacy, and in part due to this, I am convinced francis is the pope.  

Here are the relevant denzinger numbers concerning usury, you can look them up online easily. - 365, 394, 403, 448, 479, 716, 739, 1081, 1142, 1190, 1475, 1609, 1543.

It is my opinion that popes have proceeded recklessly and doubtfully into the waters of usury.  And, like with dantes inferno, popes who have inherited the problem have either been reluctant to explore deep enough for their solution or are too overwhelmed or too cowardly to do anything about it, and that is why it has not been resolved, by a pope at least.

There are three solutions I recall from memory when I researched all of this.  One, the church must define what profit is when it comes to what is regarded as lawful interest.  This goes all the way back to the montes peitatis.  The guarantee was that they would not be making profit on their interest, only providing for the overhead costs(building/personel/holding of loaned items), which was the loophole to start the banks in the first place.  However, the montes peitatis were always used to bail out the in-debt societies in which they subsided due to the usury practiced by the princes and or the populace that "tolerated" Jєωs living in and banking in their land.  So, the montes banks were turning an illicit profit imo.  And, if we all understand interest on loans to be harmful, it is hard to consider the montes banks as not being a damaging factor in theory to the society, but certainly in practice from what history tells us.  

The next solution would be that without all of the particulars(profit) defined, it is not licit to engage in any of the banking activity that the church has tried to convince itself of as lawful.  This would be argued(more commonly) from the moral rigorist standpoint when it comes to the moral probability debate(thats right, another hot debate).  

Lastly, outside of a defined montes peitaties scenario, the interest on loans practiced because of side contracts and other so called lawful elements of the contract is simply not at all licit.  And, that is because there is enough condemnation of usury prior to suggest it.  and, it is just a foreshadowing of the denial exhibited and in V2 and practiced by post V2 valid popes although concerning different issues.  Different animal, same beast.  Being that I am a sedeplenist, all these three scenarios are valid discussions for me.    

The 5% that renaissance Jєωιѕн bankers said they would never contract interest without, has now turned into a 35% by law approval the church considers lawful and their barometer(keeps rising with the ages).  Canon laws uses the "by law approval" as its barometer concerning interest.  And, just wait until you read denzinger 1609-10 about those who "appear to be in good faith".  The best the pope has to offer as a solution is - "they are not to be disturbed".

I see the same concept from the passage quoted in Jones talking about the way to make a legitimate loan and to correctly repay it:  the lender should be made "whole," by the borrower.  In other words, there is no "increase" allowed.  However, if I borrow your shovel to dig a hole and then try to return it to you with a broken handle, I've done wrong and should fix your handle or get you another one.  Even then it isn't really enough, unless I install the new handle on the shovel for you.  Thus, you are made "whole."  

How then should a moneylender be made whole without some sort of interest? 

Yeah, so in response to those 3 posts:  Of course, The Federal Reserve Bank perverts this concept, in order to justify Usury in our economy, by maintaining Inflation, through deliberate over-expansion of The Money Supply.  This is done deliberately, with forethought and malice, in order to "FORCE" people to accept Compound Interest Charges (way beyond inflation btw, but once you open the door...).  Furthermore, Jones argues, this is done to de-incentivize saving, because your savings will lose value over time, unless you "invest" it.  Of course, stocks aren't true investments, but rather wagers on how a company will perform and Bonds are loans charging interest.  Savings accounts won't keep pace with Inflation and Stocks and Bonds involve risk (as in you can lose every penny).  So, there isn't a whole lot of incentive to save, but rather an incentive to borrow money at interest and just make the payments "forever," which of course, is the design The Federal Reserve Bank has in mind for us.