Mentioning slipshod undergrad research or not in top graduate school applications?
As an undergraduate, you are not responsible for the scope and scale of research you are not directly leading. If a graduate student or PI is the one in charge of the work, you will not be "dragged through the mud" for having worked on it. In general, you are given the benefit of the doubt—you are asked to contribute to a project, and you do it. 

I don't think any committee is going to take a dim view of having published two conference papers while still an undergraduate. (And any committee that does probably represents a department you don't want to be at.)

If you are concerned about the impact, though, I would mention but not emphasize it. If you don't mention it at all, and somehow it turns up later on, it will raise more red flags than if you at least mention it in passing.