We currently have a solution developed using SSIS / C#. The SSIS package (amongst other things) has a script task that uses logic developed in the class libraries. This function
Are you absolutely sure that those shared DLLs must be deployed to the GAC? If they are in the same folder as the SSIS package, they should be discoverable by the framework without the need to add them to the GAC.
Is there no way to update your build system to avoid the version number change? If the code of those assemblies is not changing, there is no need to update the version number.
If you can't avoid the version increment, the other alternative is to build a policy file along with the shared assemblies and use that to "redirect" the SSIS package to the new version with each build.