I understand you don't want the subprocess to inherit "incorrect" file descriptors. However, there are other ways to prevent that from happening:
- you should close file descriptors as soon as you are done with the files
- you should set the FD_CLOEXEC flag on all file descriptors you don't want to be inherited, using fnctl(fd, F_SETFD, 1)

I understand that there are cases where neither these strategy is not practical, but if you follow it, the performance will be much better, as the closing of unused file descriptor is done in the exec(2) implementation of the operating system.