Some brain-storming-ish thoughts:

1) You said it "only processes the clipboard contents anyway" implying the risks are minimal, but JavaScript on web pages in IE can or could change the contents of the clipboard.

2) but since perl is activated independantly of the code appearing in the clipboard (using Ctrl-Alt-XXX in Clipboard transform keys), the risk becomes negligible.

3) To which functionality are you refering when you say "while retaining the functionality"? Executing perl code placed in the clipboard by any application? There's not much that can be done with narrow requirements. You could prepend the perl code with a password, but that's all I can think of.

4) To implement a google calculator safely, you could parse the equation yourself instead of using eval, but I don't think that's worth it because of (2) above.