Am I the only one who thinks it's dumb for there to be no built-in way to clear only user defined variables, to avoid the problem with the reset function clearing stuff like @INC?

I don't think it's dumb, and I'm pretty sure there is a "built-in" way to do it.

Is there a better way?

If I were you I'd rewrite the script. In the very least just stick it in a __PACKAGE__ other than main, that way when you reset, @INC and family won't be affected.

Would this be suitable for the Snippets section?

I'd say it qualifies as a snippet. A better solution would be to use B::Xref.