You could build some extra support to support the battery tray from below...
Before you decide to go this route, you might want to consider a few things as well...
The inner fenders keep rocks and debris from getting all over the engine, and also from denting your fender. I once new a guy that removed the inner fenders, and he ended up getting a significant "dent" on the top side of the fender, where the trie flung something up into the fender from underneath... Looked really bad with his otherwise nice paint job...
I have seen things get wrapped around suspension and driveshafts, and have them whip around beating up on the car... Not sure I'd want that stuff hitting the wiring and battery...
This about rain and wet roads, even a puddle... Thats likely to mess up an otherwise nice looking engine compartment (thats was the reason you wanted to revove the inner fenders, right?
Its personal taste, but like air shocks and high shackles for leaf spring cars, removing the inner fenders seems like a dated look... I can see "modifying" the inners, or fabricating new ones...