DISCLAIMER: This comes from someone from who never got to Commander in closed beta or the reroll in open beta, and is LtCom currently, so take it with a grain of salt.
In PvP I agree they can be a little weak defensively, which makes sense given their strengths lie in offense. But "how weak?" on defense depends on skills, equipment, and playstyles. For example, we were in Cracked Planetoid last night, with 4 cruisers (me and another engi, and 2 tacs) and 1 tac-piloted escort. We rallied back to make it a 14/14 match, and then we started circling the escort like sharks because, as he declared in team, "They'll come for me first". Which they did.
He tended to go down pretty quick when all of them would come at him for an alpha, and we cruisers tried to keep him alive with engineering team, science team, etc. We ended up losing 15/14, but it did kind of show how we were able to keep him alive longer by acting in concert throughout the battle. I'd attack his target to help pull down shields (I'm a broadside cruiser), and keep an eye on his shields and hull to keep him alive longer. He died more than we did, but he was definitely tops in damage.
So I think playstyle can affect this. Try not to get too far ahead of the team because you'll get a bunch of Klingons going for you for the easier kill. Stay close to your team support, and pick your targets well for the strafing runs. Likewise, the rest of the team should keep an eye on their fire support, and try to help them out. BoP beating the heck out of your escort? Debuff, tractor beam, pummel him, or heal your escort.
The flip side is later in another session, he was playing with us again with another tac-driven escort, and this one seemed to have much more survivability than the first guy. So I'm thinking he either had different skills to increase his survivability, or better gear and a different playstyle.