Certainly there will be times when one side will have technological advances over the other. Currently, intruders have the advantage in cyberspace. I know many experts in cybersecurity who are alarmed at the growing hacking technologies, which I am sure is partly reflexive on their part. On the other hand, many, especially in the US, consider efforts to protect public and government networks to be a nuissance, even at the highest levels of government, and governments that sponsor extensive hacking, like Russia, see it as a low risk activity specifically because of public apathy. That can change.
The writers can decide for themselves what outcome they want and what role the established technology will play in the explanation. My question with regard to this episode is whether the way the takeover was present made for good storytelling. After watching the episode, I don't find many problems with Tilly's decision: she was certainly better than Troi in Disaster. She waited, she bluffed, perhaps she could have shroomed away, but that would also have entailed risks.
My own complaint about the ease of the takeover is in how precisely the Emerald Chain was not only able to beam into the spore drive room, but also identify and surround the chief engineer and have the proper mind control tech in hand without hesitation. When Tilly called red alert, did not security guard key locations? When Earth forces beamed in earlier in the season, they had to identify the purpose of the systems in the room. Perhaps we will learn that Grudge or someone passed information to the Emerald Chain: I would find that a cheap explanation at this point. (And maybe that burr unter the arm should have been a lockout button.)
ETA; Certainly something that I wanted from the episode was a sign that the crew was willingly sacrificing itself. Put up a fight to show that you care.