That's the thing, once the Eradica goes blue you're not supposed to fight, you're supposed to run. That's the entire point of the ability- the opponent has to temporarily give up on their warpath, buying valuable time for the Advent Rebels to recover from what was likely an unsuccessful battle(as they lost a titan).
A titan level 6 ability which requires the titan to die to use shouldn't be something you just weather and shrug off. It provides you with an ultimatum: Delay your conquest by retreating or suffer heavy casualties as the price for pushing your advantage and continuing your conquest.
Also it's worth noting you should prepare for this ability: begin your retreat shortly before it turns blue rather then when it does(it's pretty easy to finish a critically injured eradica without much support with bombers). In fact having a carrier heavy fleet in general is a good idea against the eradica as carriers have more health per ship(meaning they get pwned less by chastic burst if the Eradica ever gets within range) and more importantly can kite the eradica the whole fight,allowing them easily to withdraw when the eradica dies(not to mention bombers are great for killing titans).
Also exploit the eradica's poor maneuverability when retreating. Turning on a dime away from it to run the other way gives the eradica plenty of time to shoot; by contrast fly right past it and the extremely slow turn speed of titans means you get plenty of distance on it before it even starts chasing.
Of course the best option is ending the game before the Eradica even manages to get to level 6.
Also for the record it lasts 4 minutes
