What affiliation(s) to list in an oral presentation at a conference?
I don't see this as a big deal, either way. Of course, the conference may not have a way for you to do this comfortably and might object (doubtful, but possible). You might have some contractual need to list the university at which you did the work (more likely, so check). But it is even more unlikely that they would require "exclusive" mention in affiliation. 

But I doubt that listing the smaller university is going to make any difference in whether you get hired there. It might make it easier for people to find you there over the long run, provided that  you do get hired, but harder if you don't. 

Assuming that there are no obligations that force you to do things one way or another, I'd say is is just a coin-toss. Do it if it makes you feel good.