Killing the squirrel is a prey drive thing. All dogs could do it, regardless of how sweet or aggressive they are. Its just plain ol' instinct, not a matter of meanness. Chasing and killing prey is a fixed action pattern - it's as natural to dogs as breathing is to humans. This sort of behavior isn't an indicator of aggression, especially since she's a Beagle (hound - bred for hunting!).
As far as rabies goes, I highly doubt that's the issue. I don't believe it can be transmitted by biting an infected animal. My understanding is that the infected animal's saliva has to come into contact with the other animal's blood. There is no way to test an animal without killing it. That being said, again it is HIGHLY unlikely that's the problem considering the circumstances and that rabies is uncommon in pets these days because of vaccinations and whatnot.
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