Whatever you eventually decide, don't mess with the system Perl.
Give yourself a clean install of whichever Perl you chose... and in its own dir.

Turning to your followup, "Well, I just need Perl for some scripting; using tar and scp mostly — and I'd assumed I'd shell out to those, which is why I figured I'd need cygwin installed. I also need cron or a cron-like facility to run it.":

Use Perl's native capabilities. In many cases, that will be easier (after a short learning curve on the Perl analogs) than constantly shelling out (and trying to capture returns, errors, and so on); will avoid shell-quoting issues, and will sometimes even run faster.

And as to vsespb's observation that "And perl code authors do care more about Win32 than Cygwin".... maybe! ;-) But your clientele/target audience is what matters here, anyway.

And, yes, there are many other Perl distros: Perlbrew, Citrus Perl, DWIM Perl and many more....