The same problem for nuclear: it's not self-contradictory to be eager for low-co2 energy and oppose nuclear due to its large-scale damage in case of an incident (and with Fukushima, 3Mile, Tchernobyl and various smaller incidents it's not like this is just theory).
It's similar with GMO: there are some studies showing risks and various GMO plants have been stopped due to concerns they could be harmful. Roundup is not exaxtly harmless but rather leaves ecological deserts behind - even if you are in favour of GMOs (like golden rice) you might still oppose some of them (like roundup ready plants), specifically because of doubts about the corporate-funded science by the agri-businesses behind them. Or you might oppose them on economic/social grounds, e.g. the practice of sterilising seeds which already has driven many farmers in level 1 and 2 (aka developing) countries into economic disaster.
Trust the science? Most environmentalists will agree. Trust the science funded by and the actual implementation by Monsanto? A much harder sell, akin to trusting BP's studies on climate and emissions.