dedicated input clock I/O pin as regular input in Cyclone IV

Yes, you can use dedicated clock input pins for general purpose input (but not output) signals. Indeed you can also use general purpose I/O for clock inputs too but if you can avoid it I would.

I don't think that warning is (necessarily) related to such an assignment. I've just tried this and don't see a similar warning.

Do you have a clock going into a general purpose I/O pin? I think that is more likely to result in such a warning. Quartus may find it difficult to route a clock, coming in on an I/O pin, to a large number of registers.

Cheers,

Alex