Theoretically, doubtful. The big "gotcha" that springs to mind is that Civ 3 uses isometric tiles, and Civ 4 uses actual square tiles. So while the x and y dimensions of Civ4 tiles are the same (say, 64x64), in Civ3, tiles are twice as wide as tall. If Civ3 tiles were diamonds that we could rotate 45 degrees, I'd be more optimistic, but we're talking rhombuses.
Aside from that, graphics in general would be the next area of most expected difficulty. Civ4 is a 3D game, and I expect we'd have a very difficult time getting things like unit animations from Civ3 working in Civ4. There is some precedent for 2D leaderheads in Civ4, so I'd be more optimistic about figuring out a way to convert those. Terrain would also pose a challenge not just in the isometric sense, but in the natural-looking-borders-between-tiles sense. The interface is also altogether different in Civ4, so I would not expect much if any luck migrating custom interfaces over.
My general position is that it probably would be feasible to create an infrastructure for migrating rules from Civ3 scenarios to Civ4, but it would be very difficult if not impossible to migrate map-based mods over. GameBryo being open source now might help, but if you're going to the trouble of modifying a 3D square-tile engine to support a 2D isometric layout, I doubt you'd save any effort over starting with a tool more appropriate to the task at hand.
Civ4 would probably be a more appropriate target for a Civ 1 migration.