Is it save to use the PIO in QSYS

Firstly counting pulses asynchronously is a bad idea. You should synchonise the pulse to a clock and then count the transitions on the next clcok edge.

Secondly data is moved between clock domains it must be put through a multi-stage synchroniser. Qsys will add one (transparantly) between avalon masters and slave.

Thirdly any such synchroniser can only synchronise a single bit - you cannot move the output of a ripple counter between clock domains.

So you either need to count in grey binary, or just transfer the LSB and count in the target domain.