During Vigilante missions, you have the opportunity to commit acts of terrorism by blowing bases sky high and causing tons of collateral damage, execute 'bad guys' and generally engage in all levels of debased behaviour in the name of the 'greater good' in time, becoming a villain yourself. This is no more misandrist than killing page is misogynist..
In order for it to qualify as misogyny, it has to be motivated specifically by a hatred of women. It does not. Harris' motivations are insanity and revenge for his perceived slight. Whereas the character's motivations are projected on by the player and in the case of what's offered by the game, the powers that be want the base wiped out and it's Arachnos' house and therefore Arachnos' rules. Harris does not go on rants about any women besides Page, nor does he target women besides Page.
Now let's discuss Page. As an agent of Freedom Corps, Page is supposed to see the liberation of Mercy from Arachnos. Having her suddenly turn tail and run away does a disservice to both her and the organization, especially given Longbow isn't seen in a positive light by the base at large. The fact that she's outnumbered and outgunned and still fights valiantly actually did a bit to redeem Longbow (as much as they can be redeemed, anyway. Those costumes are garish) insofar as I was concerned.
I disagree that the arc should be rewritten, especially given you have an opportunity to murder Harris immediately after. This is after potentially killing Stanzini, Fire Wire (or Psi Lass), breaking limbs of Longbow Agents, wiping out one (or two) of their installations, slaughtering a bunch of cops... You're more than welcome to cite your character's motivations as misogynist, but I honestly feel that you're chasing ghosts searching for an intent that simply isn't there.