The answer to this question may depend entirely on which religion an individual belongs to. There are certainly some who may object to the modification of plants and the changing the environment - but I would argue that they are in a very small minority. It seems clear - at least among the major world religions - that what is valued most is the sanctity of human life and the human person. Among the monotheistic religions for example, it is taught that God gave man dominion over the earth - which is to care for it, to be over it, but not destroy it. But it seems that most religious texts place a much greater value on human life. This is the crux of the matter. GMO crops may be something that preserves human life, and thus may be a good thing.
That said there are religions/belief systems that may object to the idea of modifying what is natural. While they are in the minority in the area of Burma I was in, Animists might find an objection to the genetic modification of food. They believe that all things living - plants and animals - have spirits. But they too still need to eat, and they plant rice and other crops and eat; and so far as I know they are not vegetarian or vegan. So I have to imagine based on that that even those that believe there is spirits in all things still intrinsically place more value on human life before other things.
To the people out there (that I am not aware of) who do have a religious objection to the genetic modification of crops, I would hope that they are not hypocritical in other aspects of life. That is, they don't drive cars, they don't eat farmed foods (only wild), they don't use electricity, or do anything that equally - if not more - impacts the environment. Perhaps this is absolutist of me. But I think the point is that it is actually impossible to NOT have an impact on the environment.
To be sure, we must protect the environment because we live in that environment. Historically humans have always done things that destroy the environment in the absolute sense, this is something unavoidable. But maybe if we go less absolutist, then we can say that humans modify the environment - for good or bad - through their actions. But I don't think the enemy here is GMO crops that protect the human person through nutrition. The real enemy is gas/CO2 emissions, the rapid accumulation of non-biodegradable trash, the melting of ice caps and glaciers, the deforestation of places that have always been forested, the destruction of wetlands, and the list goes on and on. These things are a true danger to human life and life as we know it. But so is nutrition and hunger. Some major religions have taken a stance on environmental protection - and I give them kudos for it.
My point is that ethics that ought to be applied to humans and maybe animals may not have to be applied to plants, and things that would in theory protect the environment - though it "protects" the environment - may also not be applied to all situations. In the case of nutrition and hunger, I would argue that any religion worth its salt - and cares deeply about the human person above all things - will make way for a genetically modified food that can meet those needs. Just because it's made in a lab doesn't make it intrinsically evil. The intention and purpose matters.
In conclusion, it is my opinion we are not playing "God" in this particular situation. We do more harm and more evil when we choose to devalue human life in preference for "perfection" as the Nazis did, or in preference for things that are naturally of a lower order; plants and animals. When we start talking about modifying humans themselves, or causing animals harm and pain without any compassion, or eradicating wild plants all together - this is where I and I am sure most religions will draw the line. And I am sure many religions may draw the line at modifying animals also - because they have consciousness, life, and feel pain just as we do. But plants simply do not.