I find it disturbing to just deactivate pre-commit altogether. If you have a look at the content of .git/hooks/pre-commit, it also checks for unresolved merge conflicts, and I would like to continue to check for those!
Towards the end of the file it runs some regular expressions that check for spaces at line endings and untidy tab characters. I just commented out these lines so it doesn't look for those, and I got rid of the pre-commit warning problem.
 55     if (s/^\+//) {
 56         $lineno++;
 57         chomp;
 **58         # if (/\s$/) {
 59         # bad_line("trailing whitespace", $_);
 60         # }
 61         # if (/^\s* \t/) {
 62         # bad_line("indent SP followed by a TAB", $_);
 63         # }**
 64         if (/^([])\1{6} |^={7}$/) {
 65         bad_line("unresolved merge conflict", $_);
 66         }
 67     }