No, it should not update your FW. (Very weird that it happened to you!) I have done several version updates and to date never had the FW update automatically.
What you can do, is look for the PKG's of the games you wish to update, download with PC and then install it through the GAME menu on the PS3.
Whether it will happen again (what happened to you with GOW), is unlikely and I don't think anyone can say for sure.
If you are worried that it might update your FW to say 3.55, then rather don't connect your PS3 to the internet. Somewhere under system settings, you can disable the internet connectivity (seeing it is reduntant if you JB your PS3 ... well ... with the exception of updating multiMAN online)