"...It doesn't mean that Allah commanded us to make war against ALL non Muslims and not live in peace with them.."

what you have said is correct; Allah has not commanded us to wage a war unless muslims are oppressed and driven out of their homes etc.; during the reign of prophet and the khalifas the non-muslims were provided protection and they had freedom to practice their religion.

So non-muslims were treated justly under islamic rule and lived peacefully however the above verses refer to having love for non-muslims which is a different thing.

So Islam allows coexistence, however the level of coexistence is also set; For example muslims can't participate in the festivals of disbelievers, they can't marry their children to them, they can't share their secrets and can't have love and friendship with them. This is what is mentioned in the above verse

And yes there are verses in context of muslims being driven out of their homes etc. but there are verses which are general also like 9:23 and 58:33 which clearly prohibit having love and affection for disbelievers even if they are close relatives. If you have a different interpretation for the quoted verse kindly explain.