I guess they would have probably promoted Data to first officer (a good new scenario for his character as well) and given Data's old bridge station to Thomas. At least that seems most logical/the easiest.
Or maybe Worf instead of Data.
Worf as 1st officer, instead of Data? I can't imagine that. Data is 2nd in command. I'd think the natural progression would be to have him assume Will's spot, & to put Worf as #1 sort of passes Data over.
In fact, depending on how Picard likes his top spots to be placed, it might not be possible to post Tom to Data's old position, in its entirety. He could man the ops post in itself, but it's doubtful he'd ever be 2nd officer, like Data, when you have Worf on the bridge, who is more deserving imho.
So either Worf would have to take over ops & the 2nd officer position, like was planned in
The Most Toys, or Worf would assume the 2nd officer role, but remain at tactical, in which case, does he remain as security chief? because I always assumed Data's role as #2 came with its own responsibilities, like a chief of operations type thing, which could place him slightly over chief of security, engineering, & sciences... maybe all functions etc...
In truth, these are all vital roles on Picard's coveted Enterprise senior staff, & is Tom ready for or deserving of that, after 8 years out of service? I suppose from a logistic point of view, the option that makes the most sense, for filling Will's vacancy, would be Data becomes #1, Worf becomes #2, & takes over Ops. Then you can maybe put Tom at Tactical, & have him take over as Chief of Security. That's the neatest layout
The problem with it, is you have now REALLY shifted the whole dynamic of the bridge crew. The whole show will look like they played musical chairs. Plus, from a character angle, these characters are now in the weirdest placement for the individuals. Worf seems suited to tactical & chief of security, but seems an odd fit for Ops & sciences. Alternatively, Data seems perfect for Ops & Sciences, but a little bit "fish out of water" as a commanding presence, & Riker as tactical & chief of security? I guess it's the least off fit of the bunch, but it still seems odd.
I suppose you could also heap Worf down with being chief of security, AND 2nd officer, AND the tactical posting, & post Tom at Ops & nothing more, but boy that really sucks the wind out of the ops post. Hmmm... maybe they didn't make the move to remove Will for good reason after all. Things get sticky pretty quick