choosing a counter method

So I'm working on a project that will essentially count the frequency of an input and while operating a led matrix via shift registers.

I've gotten used to the freqcounter library and shift register coding is straightforward enough. However I don't think it's possible to make the programs work together without hacking a serious pile of interrupts into the freqcounter library itself.

I guess where I'm at is that I need to either write some frequency counter code from scratch that will be interrupt tolerant, or I need to rewrite Martin Nawrath's library so that the matrix can be driven while measurements are being taken.

Any input on which seems less time consuming?