I disagree. The idea that it is no different from engineering your ship quite misses the mark. Engineering your ship does not circumvent game mechanics and mash them into a pulp. I find that most people who argue along these lines are unfamiliar with how Thargoid Interceptor combat is supposed to work.
While it may not be labelled directly by FDev as an exploit, it is certainly not how things are intended to work.
This sounds an awful lot like someone complaining an opponent isn't following the Marquess of Queensberry Rules in a street fight.
If the game mechanics allow it, they're not being circumvented. Intended or not, it's legitimate. Out-damaging a target's ability to regenerate/repair has been a viable strategy since the beginning of time, both in game, and real life.
Whether or not a person considers that "fair" depends on their view of the conflict as a form of sport, or a fight.