I would like my bank accounts to remain separate from my bitcoin transactions. Is using dwolla safe enough to do this? It adds an intermediary step in there.
The bank would just see money going to dwolla. Or can that be easily traced back through dwolla?
I just don't want my personal bank accounts getting shut down for some government reason down the road
Traced back by whom? Dwolla is a service started independent of Bitcoin and continues to be. It's simply a way for people to send each other money. That means it's possible to use Dwolla without having anything to do with Bitcoin.
If your local bank sees transfers to Dwolla they may guess you're dealing with Bitcoin, but that wouldn't seem to be sufficient grounds to close your account. The guidance issued by FinCEN clearly shows they don't consider people using bitcoins to be breaking the law. Now does this mean banks won't come under pressure from obscure sources to close your account for such transfers? Of course that can happen, but I wouldn't think they would do so without being able to say exactly why.
So, you're probably OK to do so, but if paranoid then use other options to obtain bitcoins.