Your best bet is to make sure you squash all the bugs prior to "shipping." It can be done believe it or not, and is not that hard to do - especially when you do not have a publisher who is threatening you with breach if you do not go gold in time to ship by X date.
Although I have not used the Pro file packer (Commercial user here), the way it is described, it seems you can actually package things into seperate resource files. This way you can have one that contains the scripts and other potentially bugged items - another for models - and yet another for sounds or what ever. Again, this is just from the way the manual reads so I might be mistaken.
The downside is that if you build it - they will crack it. Warez users do not care if you sell 10 copies at $5 each or 5,000,000 copies at $50 each. It's just the way they are, not really a matter of cost or protection used.
You can also look at the numerous third party solutions here. I recall Thinstall allows for patching of the packaged file.