yes, you have discovered the problem many before you have encountered...a lack of really cheap flights when it comes to Siem Reap and Luang Prabang.

Lao Airlines does fly between REP and LPQ for about $210 ow ai. Depends on your dates though of course, if you are going during Lao/Thai New year (mid April) things will be a bit busier and getting around more expensive.

I wouldn't want to ride in a bus for that long either.

If you haven't been to Thailand you might consider going there as it is generally cheaper to get around and there are plenty of things to see and do.