I don't think your fears are justified: I saw it happen a lot. It may happen when you kill the cpan script abruptly ("kill -9") or even shutdown the machine without leaving the shell. The lock file remains there and you may overwrite it without consequences.
It there is really another CPAN process alive, you may look for it in the process list and resume it from there. No horrendous thing comes from overwriting the lockfile. If something gets corrupt, it's only at CPAN local directory (which you find via "o conf cpan_home" and may clean up from bad files at your wish).
As a side note, the latest CPAN (1.902) is even better and offers a degraded mode to let you in without overwriting the lockfile.