Reniam,
It depends what attibute of the clock that you need. So if you absolutely need the acquistion clocks high or low state, then the only thing you can do to read it is, get it to where you can route it externally (say to PFI 0) then then externally feed this line back into a digital like, as you mentioned. Now, if you were needed it just as another clocking source, or need the frequency/period of the clock then you could just route it to a PFI line, and use the line for what ever measurement (e.g. counter measurement) you need provided that it is not actually reading the state of the line. But if you absolutely need the state (e.g. high or low), then externally routing is the only way to go. Let us know if you have any other questions, or need clarification on any of that.
-GDE