This is the explanation I like the best:
The power needed to create a time vortex took up about 99% of the sphere's power, leaving its shields burnt out and its weapons running on extreme low power. And possibly with structural damage. Remember, the Ent-E got a free ride and it was pretty beat up too. I'd say neigther ship made it through with shields.
As Picard said, "They knew their ship was doomed." The sphere may have been on the verge of collapse before it was hit by the Ent-E torpedoes.
It's possible the Borg method of generating time vortexs has a very high failure rate, explaining why they don't always try time travel.