Um, no. The Joint Development Agreement didn't have anything to do with antitrust. (You're confusing that with why IBM didn't lock Microsoft into exclusivity in the DOS contract five years earlier, which in part was motivated because of the antitrust settlements on IBM mainframes that required IBM to make its mainframe OSes available.)
Microsoft's original plan for its successor to the limited DOS was a migration path to Xenix, but, when the 1984 AT&T antitrust resolution came down, AT&T got permission to sell Unix as a product. Microsoft decided it would be folly to try to compete with AT&T selling AT&T's OS, and switched over migration plans to a product called "ADOS" or "DOS 4" or various other names in the press. ADOS would then slip under Windows, also in development, which would be the GUI.
At the same time, IBM had been trying to develop its own improved extensions and GUI to DOS to exploit 286 hardware -- Top View.
After a fairly short period of the press speculating about the coming war between Microsoft and IBM over the future of the PC, and the initial failure of Top View to get as many sales as expected, IBM and Microsoft signed a joint development agreement for what the press would, during development, still call ADOS/DOS 4, and which was internally codenamed CP/DOS. The PC would have a single, obvious software future.
And when this OS was released as OS/2 in 1987, it worked just fine on non-PS/2s, which was only to be expected, because A) IBM was already committed to customers that it would work on ATs, which is why they wouldn't let Microsoft make it a 386-only OS; and B) Microsoft actually finished development of it (and released initial outside developer machines with it) on Compaq 386s.
And it was, in fact, that 286 compatibility that hampered it the most, because the 286 had no v8086 mode to hide DOS programs in. Thus the tendency to call the DOS box the "penalty box" By the time OS/2 1.1 shipped with the GUI in October 1988, Windows/386 had already shipped and, because it used virtual 8086 mode to multitask DOS, had better support for DOS apps than OS/2. Added to the ability to drop out of Windows just to pure native DOS if necessary, the installed base of DOS apps then won the day for 16-bit Windows.
NT didn't even release until July 1993, long after 16-bit Windows dominated desktops. And NT wasn't enough to stop OS/2 Warp from making a play, it was 32-bit-extended-16-bit-Windows 95 that shut OS/2's last charge down.