Not the sort of language you're used to in church. But Amalek wasn't just one of many tribes the Israelites fought. It was, for some reason, the most hated enemy of all. The ghost of Samuel even tells Saul that it was because he didn't completely exterminate Amalek -- even including their animals -- that the LORD took away his kingship and gave it to David.
So yes, absolutely, God is love. But God is not greeting card love.
On the subject of the language of the first reading, consider this:
As long as Moses kept his hands raised up, Israel had the better of the fight, but when he let his hands rest, Amalek had the better of the fight.
"Had the better of the fight." What does that mean? It means "mowed down more of the other guys by the edge of the sword," right? So one of the lessons from this passage is:
When you don't pray enough, people die.
By "you," I mean you, the individual reading this post, and by "people," I mean real actual people alive in the world today.
Which kind of puts that whole "pray always" into perspective.