How do I switch from MultiBit to Bitcoin-QT?
As far as I can tell, BTC 0.006 is not below any relevant transaction limit. A couple weeks ago I bought a cup of coffee for BTC 0.0033 and it went through without problems.

You would probably pay a fee of BTC 0.0001 - less than 2% of your holdings, and about US $0.05 at today's prices. At US minimum wage that buys roughly 20 seconds of your time. You'll spend more time (= money) than that just reading any other answer, much less implementing it.

Short version - just pay the fee!

(Future generations reading this will no doubt, one way or the other, find it hilarious that someone could/would pay BTC 0.0033 for a cup of coffee!)