Yes, I think that they can.
In fact, in the majority of real world cases both sides believe for legitimate reasons that they are in the right.
For many things, the 'rightness' of a particular course of action cannot be determined with foresight. No intellectual process and no set of axioms is sufficient to determine a prioria whether or not what you are doing is 'good'. All they can do is point you to the right questions. The real test of goodness is always after the fact - what where the fruits of the action. Rightness is often as not simply being right, and doing the right thing at the wrong time is for the most part the same as doing the wrong thing.
This is not to say that I believe that the ends justify the means, because I believe that that is a false division and because I believe in what you might call 'the law of reaping what you sow'. Things begun with misguided intentions, false assumptions, and wrong beliefs are seldom likely to bear beneficial fruit (and even if they did that would only mitigate the harm that you caused in the process).
So, what you get is good and moral desires in conflict with each other over how those desires are best to be fulfilled. It doesn't usually help that in any such conflict at least a small but influential percentage of the people on both sides don't actually have good intentions and have ulterior motives for supporting the combat. This tends to direct groups away from solving problems by mutual agreement, and towards gamesmanship to gain advantages over the other group, ostenticibly for the benign reason espounded and believed by most members of the group, but quite significantly benifiting most especially the small group.
Real conflicts are seldom clear cut good guys and bad guys, but between good guys, bad guys, bad guys hidden behind moral facades, innocent supporters of bad ideas, misguided supporters of good ideas, good guys doing the wrong thing for right reason, good guys doing the right thing for the wrong reasons, good guys with all the right intentions doing all the wrong things, ignorant people on every side convinced of thier own moral superiority, generally innocent people caught up in evil causes, and generally evil people caught up in good causes, apathetic people fighting anything that stirs them from apathy, emotional people fighting against anything which encites fear in them, people trying to destroy the proximal causes of problems created by more distant primary causes, and people misidentifying a proximal cause as a primary cause and slamming into some good intentioned person who just thought he was trying to help.