While I haven't played the beta, I slightly disagree with you, mainly because this might encourage overly zealous spamming of these anti-Titan abilities and ships by players in desperate situations, and also because of the potential economic ramifications. But I do agree about limiting Titans combat effectiveness.
Perhaps instead of reducing its effectiveness by injuries that can be caused by excessive spamming, perhaps we could limit the Titan's ability to regenerate or regain full operational systems. For example once a Titan has been reduced to 80% HP, it can no longer regenerate its HP or SP back to 100%, and looses some of its weapons systems, and at 60%, 40% and 20% further limitations kick in. But unless it hits these threshold lvls, its HP and SP will simply regenerate back to 100% or its previous threshold lvl.
Another method might be to split the HP of the Titan into distinct zones based on its superstructure, with weapon systems and abilities tied into these zones. For example, a Titan might have an engine block which has its own HP that is seperate from the other ship areas, and can be targeted by enemy fleets once the shields are knocked down. Should it be destroyed, the Titan loses a significant portion of its ability to move and use any abilities that has anything to do with augmenting maneuverability.
To regain full operational status, they will have to report back to Foundries for extensive repairs, which should cost you a fair bit of resources like you said. But regardless of dmg, they should still be able to escape via phase jumping.
I also like your idea of using the Anti-Structure ships to shoot at them, since technically, Titans are nothing more than mobile, super charged star bases. I mean, Titans should be destructible by something other than a Titan, and since they're WAY BIGGER than almost any structure, you should be able to shoot it with anything but super weapons.