I've been thinking about the issue a lot over the last few days and I've come to the same conclusion. Lossless conversion would be nice, but there are just too many issues with compatibility for it to really be feasible. Power loops are a pretty bad exploit when you take mod packs and servers into account, so with that in mind, I'll be adding config options when I get a chance.
By the way, do TE conduits not work properly with IEnergyHandlers that have faces that both output and can intake energy?
An implicit assumption we make is that a given side either outputs or inputs energy - this is why conduits are no longer sided, but Energy Cells are. There's no great way to handle something that does both without changing conduits back to the blue/orange thing. So what is happening is that you are pushing energy to the conduit, and the conduit pushes it right back to you, since you accept energy on that side.
Frankly, I can't really justify a block doing both things on a given side at the same time, sooo...
If you want to fix it on your end, you'd need a flag that basically states if a given side is sending or receiving for that tick, and short circuit your receiveEnergy function appropriately. There's literally no great way to do that, because either you'd have to put that logic in, or we would, and if the onus is on the conduit, it would involve complicating the API and greatly slowing down the process with function calls.
