I know that in vanilla Minecraft it is impossible to automate the creation of Withers by using pistons. Is it possible in FTB?
A reusable, automated setup is possible with the use of a ComputerCraft turtle and a Modular Forcefield System:
This uses a custom-programmed turtle to place the soul sand and wither skeleton heads on request, then activates the MFFS. The MFFS creates a forcefield with damage upgrades, which both contains and kills the Wither. After a set period of time (which you have to figure out and hardcode into the turtle, depending on the specific upgrades in the MFFS), the turtle turns off the forcefield and collects the Nether Star.
The soul sand, wither skeleton heads, and coal are retrieved by the turtle from surrounding chests. The MFFS is powered by forcicium. The video doesn't automate the supply of those resources, but the heads and coal supply could be fully automated, while the forcicium and soul sand supply could be semi-automated with quarries/RP2 bores and ender chests.
Use the following setup:
That's a Redpower Deployer, filled with wither skulls (you only need one).
Press the button, or apply a redstone pulse, and hey presto!
Obviously, if you have a lot of wither heads to get rid of, you can easily build a simple wither head disposer thusly: