When in doubt, it’s often useful to suspend judgement and list as many variables as you can, this situation is no different.  

 

1. Since it’s probable that a majority of Crimean citizens want to join Russia anyway (I write this before the referendum participation % and outcome are known), you either make them happy and a minority unhappy, or it’s the other way around.
2. The Crimea used to be part of Russia anyway
3. However outdated a concept, it’s Russia’s “back yard”
4. We can’t stop Russia anyway. The US is relatively exhausted by two very expensive wars with very dubious results and a financial crisis to boot. The EU has too many problems of its own (euro induced) and is financially and militarily weakened.
5. What are we’re going to do anyway? Not fight, surely.
6. Sanctions are likely to hurt us considerably as well, depending on how Russia retaliates
7. We need Russia’s cooperation in other fields (Iran, Syria, North Corea, nuclear non-proliferation, fighting terrorism, etc.). Perhaps it’s better to concede Crimea in return for favors/concessions elsewhere.

1. It’s a flagrant violation of international law, territorial integrity (the latter guaranteed not just by international law but by a 1994 treaty in which both Russia and the US guaranteed the borders of Ukraine in return for the latter to give up nuclear weapons).
2. If not stopped here, who knows what Putin’s next step will be (the ‘1938 Mnchen’ argument).

This is certainly not exhaustive. Feel free to add/detract/comment, here