Is it safe to delete the 32-bit Intel code from apps using a tool like Monolingual?
Yes, but...

You may develop problems updating certain apps as removing parts of the app using Monolingual can render the code signing of the application incorrect.

From Switcher's Blog


  OS X 10.5 Leopard brings a new Code Signing security feature that helps verify the integrity of an application. Applications are signed by their creators before being distributed using their private key, and then can be verified on the customer's machine using the companies public key.


That's for third party apps. I really wouldn't tempt fate by doing this to system files.