I don't like this statement at all. If the implication is that people of the opposite sex will have ulterior motives because they'll be sexually attracted to you then this ignores gay and asexual people's existence. It also assumes that straight people will somehow necessarily be sexually attracted to anyone of the opposite sex. So I guess she shouldn't trust male family members either?
While yes, people (not necessarily those of your opposite sex) can screw you over and take advantage of you when you're vulnerable, you also have to be vulnerable at times. Nobody can live truly independant of others. We all need to be able to trust at least a few people even if it'll make it easier for those people to take advantage of us. If you can't trust anybody, you'll inevitably run into a situation where you need help, but no-one's there to offer any.
I hate that Misato ends up agreeing with what Konishikawa said. We need at least one person to push back against this narrative ASAP, or I'll lose all faith in this comic. It's such a shame too, because it did have some profound things to say from time to time, especially regarding (sexual) harrassment in the workplace.