So you still had weight on the other spring?

If you had the entire axle hanging so the springs were fully unloaded there wouldn't have been any pressure on it. Normally you disconnect the shocks and sway bar, then drop the axle down as far as possible without over extending the brake lines (sometimes you need to put the axle on another set of jack stands). At that point, there's no pressure on the track bar.... to line it up you just use a floor jack to raise the passenger side up until it's where it needs to be (and pull the axle left/right).

There's a trick for aligning the front track bar in SFA vehicles... put the vehicle back on the ground and have someone turn the steering wheel; that shifts the axle over and makes it easy to line up. I know, it doesn't apply to our XKs/WKs... but there plenty of members here with XJs and Wranglers that may find that truck useful.