Only workaround I can think of that should work is:
1. Work with the mojoPortal source code not the pre-compiled deployment packages
2. Don't use inline code, put your controls into your own VB.NET project and use code behind so that the VB code is compiled into a dll and use a post build event to copy the dll to the Web/bin and copy your .ascx into your own folder. See the post build events in the mojoPortal.Features.UI project or WebStore.UI project for examples
3. Use project references to mojoPortal rather than dll references and in those cases if you do reference a dll, in the reference properties set Specific Version to false.
Hope that helps,