These are all pretty reasonable factors.
I hope (probably in vain) that some suit in Paramount won't say "We left $600m on the table with STID vs IM3 or MoS, and therefore we can't count on it for a summer tentpole", leading to serious budget cuts and a probable Holiday Season release for the next movie. Don't care too much about the release date but I'd worry about the budget cuts w/r/t production values.
I doubt that another movie is off the table.
I wouldn't worry too much about Star Trek XIII. Ultimately, Star Trek XII will do better than Star Trek XI once everything is counted (it's already looking that way now). If there is a reduction in budget for the next movie, we probably won't notice unless it's like half or something.
Interesting the production team has been quiet since opening weekend. I think they're in a state of shock.
I don't know why they would be. They probably just moved on to other projects.