Having given it a lot of thought I frankly think it's far more likely they trade Baez. Baez was a player they inherited. McCleod has also mentioned when he was with the Padres he wasn't prepared to draft Baez had the cubs passed on him. When you consider the types of players the front office has targeted in trades/draft, Baez really isn't the same type of player.
Also consider Theo's history with the red sox. Hanley Ramirez was signed in 2000 as a amateur FA pre-Theo. Theo traded him after the 2005 season with Anibal Sanchez, Jesus Delgado and Harvey Garcia for Josh Beckett, Mike Lowell and Guillermo Mota. Hanley prior to the 2005 season was the #10 prospect according to baseball america. Sanchez wasn't ranked in 2005 but prior to the 2006 he was ranked 40th with Hanley being the 30th ranked prospect. Beckett would be going into his age 26 season in 2006, Lowell into his 32 season after all star season in 28-30 though he did miss the all star team the year prior to the trade. Beckett was coming off a 4 WAR season and Lowell was obviously coming off a down year. The 2005 Red Sox had some pitching with Schilling but with David Wells, Arroyo, Clement, and Wakefield being their other 4 it was clearly needing an upgrade.
So, clearly this wouldn't be an unprecedented move for Theo to make. Additionally, when you consider the fact that they've barely played Baez outside SS at all it makes me question the motivation. They've gone out of their way to say Castro is a part going forward. So, unless they are outright lying, SS isn't an option and yet Baez remains there. The assumption has been 2B given they've toyed with Alcantara in CF. I'd present a different idea. What if they are mentioning other positions as options yet keeping him at SS the majority of the time as a way of keeping leverage. If it was clearly obvious they had an extra piece they couldn't play in a position they would be dealing from a poor position and with SS clearly being the more valuable position having Baez spend the majority of his time there makes him a more valuable trade piece.
Also, if you remove Baez from the equation, the only prospect piece that doesn't really fit is Russell. Bryant can play 3B. Alcantara can play 2B and you have 4 options in the OF with Almora, Soler, Schwarber and McKinney. As for Russell, you have at least 2 years before he's ready for the MLB. That buys you a bunch of time to get a clearer picture. Maybe Russell doesn't work out. Maybe someone else doesn't. Maybe at 27-28 they consider moving Castro if everything goes right. And at the end of the day if you end up trading Baez for a high tier starter that leaves you in a similar position to what you would have been had you signed Shark. Hypothetically, let's say they go after someone like Mat Latos who's a 2016 FA. If they give up Baez and a McKinney level piece and perhaps something else marginal you're really not losing much if any value and you likely set yourself up in a situation where they likely would take Russell over Baez and have a pitcher they likely can re-sign long term.
Pure speculation obviously but to me that makes the most sense.