Yesterday I got rearended in the 11ft long flatbed trailer behind my Toyota Avalon, twice within a couple minutes, both by humongus new pickups. One was at a stoplight. The other was at a stop sign.
The trailer did get a little bent but I think it will be ok.
Are you sure it didn't damage the structure of your car due to the impact?
However that probably should not affect alignment settings
Well, hopefully... I remember some tow hitch makers stating it could actually protect the cars from damage in case of a minor crash, yet it was not true at all...