It's the classic problem of the ends not justifying the means.

In this case- if you take an army of undead to defend a LG Paladinic stronghold or save innocent lives or what have you, you still used negative energy to create the undead in the first place, and thus it is an act of evil. The prime argument used here is that if you had enough power to do good via an act of evil such as necromancy, you could have re-focused your power to some non-evil means to the same end.