Time Machine is pretty reliable and I'm using multiple Macs with it to my FreeNAS box. I've had the corruption issue that you mentioned before, even with Apple's own Time Capsule. The reason, as you guessed, is the network disconnect. While Time Machine does a good job with interrupted backups and restarts, the underlying filesystem is the problem. Basically Time Machine needs a full blown HFS+ filesystem to work, you can read
here for some limitations of HFS+. On top of that in order to guarantee TM gets a full HFS+ filesystem to work with it create a sparse bundle on whatever it's storing the backups on. So if HFS+ flakes out
OR your Wi-Fi drops while writing one of those 8MB bundles, you have a corrupted HFS+ filesystem.

TM does do some automated repair work and some clever things with Time Capsules to minimize the damage, but it's still a problem. TM has also had issues with when the underlying filesystem it's storing the image on is running out of space/hitting quota although it's better than it used to be.
You can look here:
http://pondini.org/TM/A5b.html for a guide to repairing the TM filesystem image, it's the same no matter how the bundle is stored. Ironically the one place it's very difficult to repair is a Time Capsule, because getting access to the underlying sparse bundle image is a PITA.
Bottom line: IMO you need to fix your Wi-Fi...
I have multiple MacBooks happily backing up with Time Machine to multiple destinations simultaneously, including FreeNAS. They do it via Gigabit Ethernet if at a desk, or via Wi-Fi when elsewhere including the sort-of-wake-from-sleep sessions. You don't say what version of OS X you're running and that can also make a difference as there have been a raft of TM patches and improvements over the last few versions. As of June 2014 I'd suggest the current Mavericks 10.9.3 if you can.
One last suggestion: turn the AFP service off and on again on the FreeNAS box to force the Macbook to redo all it's AFP connections and see if that avoids the "corrupted" issue.