Vex follow the Pattern. When things don't line up with Pattern they fix it. When things are following the Pattern they don't care. If you aren't upsetting the Pattern the Vex have no reason to attack you.
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You could also say that the guardian was vital to help fix the pattern. Be cool if there were missions where you fought with the vex side by side.
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We could've been neutral with the Vex, just like before the Collapse... but ya had to get your hands on that gun...