It's not though. The founders were in may ways more liberal than these guys. In some ways, a lot more liberal. I mean, they left out God and Christ out of the Constitution, quite deliberately.

Is there a de facto separation of leadership at the very top and lack of effectiveness/efficiency just due to another "agency" having the lead?

In that case, the proper response is not to gut the agency in question, but to consolidate its activities with those of a related agency and then save some of the administrative overhead costs.

But that's not what they are proposing. So that might be your point, but it's not the point of your party.

systems across the country according to a predictable, fair set of standards? 

Yes, you do need an agency to handle that kind of project. 

The point is ...federal funding for research can be provided without the setting up of an entire federal agency.

While you're right on general principles with this statement, in this particular case, there seems to be NO "private"/non-governmental body carrying on this branch of research. I suppose, if such a body* existed, there might be a rational argument made for funding its studies, in preference to maintaining a government agency to accomplish the same goals (btw, I don't think the argument would necessarily be valid - outside of the mindless knee-jerk opposition to "government" so prevalent with Republicans these days - but it could be made). Especially when one is talking about practices and standards that affect the nation's hospital system as a whole. 

But, since there isn't, AFACBD, any non-governmental entity doing this, it seems that keeping the AHRQ going should be debated on its own merits: and, for me, closing down agencies like AHRQ on BS "budgetary" grounds is both stupid AND evil.

*Maybe something called the Foundation for Infectious Disease Detection, Limitation and Eradication?