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 }