I'm not an authority, and this is strictly "FWIW".
If an identical car to yours in all other respects was presented at the same time with the TSB followed "to the letter", your implementation of the AIR pump deactivation would be the less-correct method.
The bulletin leaves everything in place, blocks the air flow path, and re-tunes the PCM to eliminate the AIR pump cycle. A rather messy approach, but I think it was done to prevent any issues with states having under-hood visual inspection pass/fail criteria AND to achieve the change at minimal cost/shop time.
Removing the pump and plumbing certainly looks better. The lack of a non-standard manifold fitting "spec" plug (ie. a GM PN for that purpose) means there are going to be different visuals for anyone that has gone the "removal" path rather than strictly following the TSB. Some methods I've seen to plug the manifold ports were much less attractive than others, and if I was judging a stock-class group, it might be worth a comment, if several vehicles had used different methods of plugging the manifolds.
This is not to say I think you should put the plumbing back on the car--if it was a Corvette, with the anal-exam level of scrutiny for competition judging purposes followed in that arena, you would get nailed for the way the TSB is implemented on your car at present, but I think the B-body community is generally much more tolerant of reasonable interpretations that carry out the intent of the modified configuration, even if the TSB lacks specific instructions to remove anything.
Proceed with caution, but don't let my comments make you think you need to put all that crap back on the car!!! But I WILL be looking for the position of your valve stems when I see that car....
(private joke between Jim & I, folks--Bowling Green 1999)