Not sure exactly which rough country 2.5" kit you are ordering but they all function basically the same as other aftermarket kits.
I personally have an '07 Rubicon JKU as well. The electronic swaybar motor controls whether the swaybar rotates as a solid arm or independently. The motor will not disengage the solid swaybar rotation in an electronically disconnected state unless you are in 4 wheel drive.
With the rough country kits that require swapping out the swaybar arm links, this is due to needing longer links to connect the swaybar to the axle in a horizontal plane from front to rear of the jeep and the link running vertical from the swaybar arm down to the axle.
Here's where it becomes an issue with the Rubicon electronic disconnects and aftermarket swaybar links that I have seen in person happen to three Rubis. With some kits, the links tend to be right at the required length with out any extra extension to them (8-10") depending on the lift size. When you off-road through light articulation conditions the electronic disconnect works and functions as designed with no issues.
However, when you get into areas that require more articulation, without limiting straps the swaybar and link can "flip" from the upside down/backward "L" position to a normal "L" position. When this happens, the link lays right over the tie rod. Then when you turn your steering wheel, the bolts/bracket on the driver side end of the tierod snag the swaybar link and bends them.
This is why you see a lot of guys either running the Rubi e-disco for normal trail use along with manual discos for more difficult trails (like I do), or sell their e-discos all together and buy other swaybar systems like the Currie Anti-Rock system