First of all; the original acquisition is not what I was referring to, but rather: Microsoft's "maintenance" of the Halo IP after Bungie itself left Microsoft's domain, and the formation of a near-entirely new studio (343) to develop it. Ok, they didn't buy the IP at that juncture; they bought a studio to develop an IP they already owned. Use some creativity and you can see the parallels are similar enough.
Second: Do you recall the keynote where Bungie unveiled Halo for the first time... at MacWorld 1999? For reference, Microsoft acquired Bungie in 2000. I've literally never heard the assertion that Halo was intended to be an RTS; my understanding is that it was originally going to be a third person FPS, as the 1999 MacWorld trailer suggests, but was changed to a first person FPS when Microsoft purchased them.
https://www.youtube.com/watch?v=6eZ2yvWl9nQ