CathInfo.com

It would seem that a heretic baptizing an infant (of say, Catholic parents) in danger of death is valid and the effect conferred if the correct matter and form is used. I would think the intention to "do what the Church does" is fulfilled here. In other cases, it is not as clear.

Eh, that's a contentious question, which is really why such situations should be avoided by any means possible.  Could the sacrament be coferred validly?  Sure, I believe so.  Does it necessarily follow that it would always be conferred validly?  I would say in the case of baptism, so long as either there was a compatible interior assent (i.e., the minister's theology held baptism to be salvific) or the minister had the sacerdotal charism, I would accept conference as being likely, or at least less than gravely doubtful.  I would posit that the barrier of proper conference in the second quote of Thomas Aquinas has to do with the willful act of receiving sacraments from one formally in schism (in the case of receiving the Eucharist or an adult baptism).  However, I would consider the case of an atheist or one denying original sin or the necessity of baptism, to be suspect in the conference of a baptism in the abstract.  Of course, it seems to me unlikely that someone denying original sin or its remittance by baptism would bother, especially in an emergency setting, to baptise the child.  If they did so, it would logically follow that they believed there was a grave spiritual need to do so, and that the baptism fulfilled that need.  It's probably a moot consideration.

If I'm not mistaken, weren't some converts from heretical sects NOT conditionally baptised when they converted?

Sure, conditional baptism is examined on a case-by-case basis, to determine if the form, matter and intent of the original minister was sufficient to confer the sacrament.  For those baptised by a minister who possessed the intent properly formed by the theology of original sin and the laver of regeneration (Orthodox or other schismatics, Lutherans, Methodist, some Presbyterians, etc.), or have the sacerdotal charism necessary to correct the defect of faith by virtue of acting in persona Christi, the baptism is probably going to be considered valid.

As atheists can baptize validly, it seems clear that explicit, personal desire (on the part of the minister) to remove the guilt of original sin is not necessary.

I find this statement odd, and at odds with both the teachings of Aquinas, and this remark which I found in the Catholic Encyclopedia regarding sacramental intent:

The Church teaches very unequivocally that for the valid conferring of the sacraments, the minister must have the intention of doing at least what the Church does. This is laid down with great emphasis by the Council of Trent (sess. VII). The opinion once defended by such theologians as Catharinus and Salmeron that there need only be the intention to perform deliberately the external rite proper to each sacrament, and that, as long as this was true, the interior dissent of the minister from the mind of the Church would not invalidate the sacrament, no longer finds adherents. The common doctrine now is that a real internal intention to act as a minister of Christ, or to do what Christ instituted the sacraments to effect, in other words, to truly baptize, absolve, etc., is required. This intention need not necessarily be of the sort called actual. That would often be practically impossible. It is enough that it be virtual. Neither habitual nor interpretative intention in the minister will suffice for the validity of the sacrament. The truth is that here and now, when the sacrament is being conferred, neither of these intentions exists, and they can therefore exercise no determining influence upon what is done. To administer the sacraments with a conditional intention, which makes their effect contingent upon a future event, is to confer them invalidly. This holds good for all the sacraments except matrimony, which, being a contract, is susceptible of such a limitation.

It seems that while a virtual intent is sufficient to confer the sacrament, this intent would by definition have to be ratified by a previous volition that the minister understood and assented to the effect of the sacrament being conferred.

In danger of death is not usually something that can be avoided of postponed.

Certainly, but historically in hospitals, especially Catholic institutions, priests have been present to perform this function as needed.  Naturally, there are, as you say, cases of unavoidable necessity.  I suppose in those instances, we must simply trust to hope.

Are you calling into question what the Church clearly instructs in a situation where there is a danger of death? Are you sure this really never happens?

I'm not sure I follow what I'm calling into question.  As for the frequency of such a thing, happening, I find it odd in the extreme, at least from a logical standpoint.  If the child had parents that were Catholic, then they would baptise the child, not their atheist acquaintance.  I just find it difficult to imagine that an atheist, having no impetus, would choose of their own volition and desire to perform on a dying child a spiritual rite of a religion they don't believe it.  I'm afraid that doesn't seem likely to me.  

Yes, but you seem to be applying this to other situations in which the Church seems to have already decided.

Can you quote some text that explains it the way you interpret it?

Can you clarify what you're asking?