Some Suggestions on JR module's update method/approach
Using Jamroom
This really shouldn't be an issue for you:
1) Go into the ACP -> Core -> Marketplace -> Global Config
2) Set the "Marketplace Versions" to the number of versions you want to keep - i.e. 2, 3 etc.
3) Run an integrity check and it will be "cleaned up".
My guess is you have that setting set at "Keep all Versions" and have just never changed it.
Let me know if that helps.