I agree that some parts in Hondoori's translation are a bit too much literal, and rephrasing some of them in order to make them sound more natural is a good idea, such as the example above. However, I don't think using bad words here is a good idea.
I'm not sure if even the "pain in the ass" part is a precise translation. Maybe, in the original, it was something similar to "mendokuse [面倒くせー]", which means literally "troublesome", and that's why I put this sentence as something in the lines of "capturing him alive is a troublesome task".
Besides, even if indeed Vile / Vava meant to use a bad word here, I haven't seen a single bad word in the entire megaman series (at least not in the original localization). And the classification for most megaman games are Rated "E" (everyone), not "M" (mature). IMO, avoiding bad words would be wiser.