First, I\'m loving the very clearly delineated versioning of the SSIS tools. >:(
I installed SSDT BI for Visual Studio 2013 and built a nice little project in it to
To answer your question directly, no, there is no way to fix the issue in the .ispac file. The dtsx files are different in a couple of ways in SQL Server 2012 and 2014. The only solution I found is to downgrade my packages from VS 2013 to VS 2012.
In case you've already developed significant work in Visual Studio 2013 only to realize that you can't deploy it on SQL Server 2012, I found a workaround how you can "downgrade" your SSIS 2014 packages to SSIS 2012. I wrote it on my blog here:
http://vaniecastro.com/2015/02/26/how-to-downgrade-sql-server-integration-services-2014-packages-to-2012/
The idea is that you need to manually modify the XML file, change the PackageFormatVersion and replace ExecutableType property and componentClassID attribute values to use the DTSX2 Version 2012/01 values instead of the DTSX2 Version 2014/01 ones.