Had it happened, I'm not entirely convinced the licensed characters would be segregated into their own individual universe. Yes, that was what Marvel did with its later acquisitions, but those were all in the future. Shooter's summary of the situation likens the proposed to deal to the same licensing arrangements Marvel had made in the past: notably properties like Transformers and Godzilla. The tendency was to integrate those characters in the proper Marvel universe, so much so that you still occasionally come across things like S.H.I.E.L.D.'s anti-Godzilla mobile artillery platforms in contemporary comics (with the only the minimum of changes made in order to get around the fact that Marvel no longer has the license).
At bare minimum, I expect that the appeal of crossover stories would have ensured that the licensed books weren't keep too isolated. The properties are too well known to avoid that, unlike, say, the Malibu acquisition a decade later.
Beyond that, though, it's hard to say how it would shake out. DC really created the idea of the line-wide crossover/event with "Crisis on Infinite Earths", which still hadn't happened yet. Without that, I'm not sure there's precedent for the sort of massive retcon that would properly integrate the two continuities. It could still happen, of course, but it's without any real precedent. It could just as well look like DC's acquisition of the old Fawcett Comics characters in the 1970s: broadly maintaining continuity with the past but allowing for crossover stories.
I'd be interested in how this affects comics going forward, though. In the late 1980s, DC famously sought out British writers based on the critical success of Alan Moore's work (particularly Swamp Thing and Watchmen). This brought creators like Neil Gaiman, Grant Morrison, and Peter Milligan (not to mention paving the way for later arrivals like Mark Millar) into American comics for the first time and formed the nucleus for DC's Vertigo imprint, which revolutionized a lot of things about the industry (increased reliance on trade paperbacks, licensing, etc.). Without Moore's work at DC in the early to mid 1980s, this is unlikely to have happened, since it was apparently a deliberate decision by DC to court these writers.
Regardless, the American comics industry still is liable to run into a prolonged slump towards the tail end of the 1990s, and Marvel's business problems that led to its bankruptcy during this period are unlikely to go away. If the DC properties were licensed, as opposed to purchased outright, it's possible that Time Warner buys out Marvel here, similar to the later Disney deal. Otherwise, I'd expect the licensing arrangement to end, with Warner licensing the properties to some other company or giving up on periodical publication altogether.