I don't think balance is an issue you're going to be able to address well in a multiple-mod-interaction setting. The issue most people seem to have with lava pumping isn't the MJ side of the equation, but the EU side of things, and you're already into at least three mods for that to be an issue (BC, IC2, TE). When you look at the possibilities for infinite renewable EU and MJ with three mod interactions, the lava pump isn't that grand a solution compared to others. Off the top of my head, Steve's Carts can provide renewable power by creating an infinite charcoal chain with IC2 and BC. People speak of the lava pump as if you can have it going the instant you make a world, but the reality is that it requires about the same resource and time investment as an automated tree farm providing infinite charcoal. The ease of set up on the nether pump is currently low because it has been featured in a number of popular videos, and people would rather copy a system known to work than experiment with their own systems.
As far as fixing the unsightliness and the server lag, perhaps the pump could be modified to only extract half a bucket of lava per lava source block, and replace the source block with cobblestone when it does so. You could even take this a step further for balancing, changing the power requirement of the pump to perform this action to something in the thousands of MJ per block (4.5k would be a good starting point IMO, costing 9k per bucket and creating a 9k profit per bucket pumped), and perhaps requiring a water source to perform this function.