You did not say what distribution that you are using. If your distribution supports any of the Debian, RPM, or Slackware package systems then you could use checkinstall:
Your procedure would be:
Compile the program on the development system.
Use checkinstall to create the appropriate package.
Install the package on the target system.
Using this method the newly compiled programs are never actually installed on the development system.
As to the target libraries being different from the development libraries, you might be able to get away with installing the development version of the target libraries on the development system even though the development packages on the development system would not necessarily correspond with the binary libraries. You would have to override dependency checking when you installed the devel packages on your development system.