I think there's definitely more to it. In an early episode when Wells was looking into the future with his device, there was a headline about the Flash still missing. My inference was that the Flash is needed in the future and something has happened to him (dead? missing? powerless?) and Wells is very concerned with righting this and making sure the Flash is happy and healthy and well-trained and ready to fight evil. But his character seems like one of those "the ends justifies the means even if it means killing a shitload of people if it means I save even more shitloads of people". He seems like the kind of guy who could rationalize killing Barry's mother if it means Barry ends up saving millions of lives in the future.
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