You're asking for function separation in Perl/Tk? Well, just do it! It's the same as in normal non-GUI programming. You can use subroutines, you can use modules. Granted, there are some nice features in Tk which allows for writing quick scripts (e.g. -variable, anon subroutines in command bindings), but nobody forces you to use these features.
This is just like people complaining about Perl to lead to unmaintainable code. You can write unmaintainable code in both Perl and Perl/Tk, but you can also write nice code if you use the language and module wisely.
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