There is room for much improvement...

1. selecting the region:

a combination of backward-up-list and mark-sexp will select the surrounding structure (repeating will extend the selection till statement (ie. ';') boundary.

(please note that cperl-mode injects here some semantic knowledge about the code's structure which can't be reflected in a simple regexp rule)

2. the rule for align-current has the advantage to harmonize the surrounding whitespaces too. And align-regexp seems to allow the same extended logic.

So combining both steps bound to a key should make alignment of fat-commas quite easy.

I experimented with a kmacro and it seemed quite nice. :)