I think the Whale Probe is gonna fuck us over. Just think of what needed to happen in order for the Enterprise crew to save the day!Well you're not thinking about ALL of the ramifications. It's possible now that the Federation might not meet the Borg for a long time after when they did. remember, Q flung the Enterprise-D into the Delta Quadrant which is where they met the Borg and the Borg got a "taste" of the federation. It was either Q or someone else that said we weren't supposed to meet the Borg yet, so it's possible that the Borg aren't encountered for some time.
You have to think of it as the butterfly effect. One thing has changed, the destruction of Vulcan, many many unforeseeable outcomes will arraise from it. (namely writers can do whatever they want) Though I think certain things should still be in place, V'ger visits Earth looking for it's creator, The Whale Probe visits Earth, but those will have different outcomes now depending on all the actions that lead up to it.
Kirk had to maroon Khan on Ceti Alpha V. Years later, Chekov had to rediscover Khan on Ceti Alpha V. Khan had to steal the Genesis device. Spock had to die. Spock had to be reborn on the Genesis planet. Commander Kruge had to try and steal Genesis. Kirk had to blow up the Enterprise and steal a Bird of Prey. They had to take the Bird of Prey all the way to Vulcan (which doesn't EXIST ANYMORE!). Then they had to fly home to Earth, only to be stopped on their way and figure out that the transmission from the Probe was the sound of humpback whales.
That Probe will destroy us all.

Lets hope they come up with another solution!