You can work on alignment file, which is in fact text file. If you'd like to modify it you may be interested in some text scripting.
You cam also modify alignment in seaview as it allows for sequence edition. I don't know what automation you are thinking about. As I understood you'd like to optimize the alignment to prevent secondary structure disruption. So you need to have secondary structure visualized in real time. But that is what you get with seaview - you have both - MSA block and respective SSEs block displayed simultaneously and you can move them both to adjust the alignment.
But if you need to recompute SSE every alignment alteration, my method wouldn't be efficient to do so. Seaview only visualizes sequences. Do not perform any additional computations on them. I'd rather suggest not to compute SSE basing on adjusted alignment but rather on SSEs profile comprising predictions for every sequence in the alignment (you do not need to recompute SSE but just observe how profile behaves).