It seems obvious to me that the timeline has been altered since the events of First Contact
- Who knows what kind of Borg/ Ent-E debris were subsequently discovered and reverse engineered.
We never actually see the crew of the 'E' get home after ST:FC
. Perhaps it was like Back To The Future II
, and they returned to a universe where Q owned a bikers casino and was sleeping with Picard's Mum. Inssurection
must take place in The Nexus(TM).
This would explain why the previously never heard of Archer
seems to have had such an important role in this NUniverse - His dad actually found something that enabled him to "invent" the warp five engine early.
So to answer the original question, the technology is way advanced and the Ent-E would be defeated.
Though I still can't figure out why the Wormhole Aliens (TM) never saw this coming/revealed it to The Sisko. Perhaps he will return in the next movie to sort the mess out.