Lets see:
Chimezie Metu was taken with a 49th pick (if you're super interested in a guy, you find a way not to let teams 48 chances to snatch your target), whereas with Branham (no. 20) the Spurs admitted to exploring options of trading into the late lottery to grab him because they feared he wouldn't be available. That speaks of a very different level of interest in each.
On top of that, Chimezie Metu played about 5 MPG as a Spurs, scoring less than 2 points his first season at 21 years old. Meanwhile, Branham is one of the fastest rising rookies, scoring over 10 PPG on good efficiency (44% FG, 83% FT). That speaks of how much each measured up relative to their expectations.
All in all, I don't think the interest level and subsequent performance of each merits using Chimezie as a reference for anything regarding Branham. Furthermore, it'd seem nonsensical to me to put his future with the franchise in question because he's competing for minutes with a guy who's about certainly on his way out of the franchise by the trade deadline at most like Graham. If Branham doesn't meet the required standards at 19, then you keep working with him until he does. Spurs don't give up on first rounders like that unless they're basically bums too lazy to run at 20 (Samanic), or start a penis flash parade in each city they go to (Primo).
In the proposed scenario where we draft a Thompson (I'd be shocked, but can't rule it out), actually I don't see Branham losing the nod at all, because he'd be a good complement of him. I could see it if, for instance, we took Keyonte George, Hawkins, or someone in that mold, whose skill sets are redundant. If you take someone like that and they clearly overtake Branham, then yes I could see one of them being moved, in the same way that I could see the Spurs taking any talent they deem better than who they currently have at whatever position, as it should be when rebuilding. So I wouldn't key in on Malaki in that regard, since he's as susceptible as any other youngster to being moved in the right cir stances (but not dumped).
In short, provided there's some coherence and stability in the thought process of the FO (no reason to doubt it), you don't trade (for the first decent offer) a guy you were recently willing to pay a high price for and exceeded expectations.