So, in real life, a battlecruiser or fast battleship with long-range 14" guns and 26+ knots of speed could 'kite' a squadron of 12"-gunned, 21 knot early dreadnoughts basically forever and engage them from beyond the distance that they could return fire. But they wouldn't be able to sink very many, if any, because, in real life:
Ships have limited ammunition.
Long-range gunnery before radar fire control was horrendously inaccurate.
Eventually, weather or nightfall will artificially limit engagement ranges, forcing them to close in or withdraw.
Long-range gunfire would likely bounce harmlessly off battleship-tier armor, as opposed to Aurora, where all armor is ablative.
If you want to make it so that a single beam destroyer can't destroy a fleet of beam battleships, you could try to adapt these factors to Aurora.
Limited ammunition:
Beam weapons now consume some form of ammunition, whether that's ionized gas, duranium slugs, or reactor fuel. Make it completely separate from the engine fuel, and produced at a certain rate without cost by maintenance facilities. Unlike missile magazines, beam magazines are inert and nonexplosive.
Accuracy:
Increase base beam range, while simultaneously reducing beam fire control range. Basically, make it so that most beam weapons' ranges overlap more, and if you're on the edge of engagement range, hits are unlikely and do so little damage that shields will protect you - except maybe for specialized long range weapons like particle lances.
Space weather:
It might be interesting to introduce dynamic "weather" effects, like 'aether storms' or whatever, that could have a deleterious effect on beam combat. Maybe it'd be interesting if planetary gravity wells were hotspots of aether storms, and an outgunned fleet could seek refuge by hiding in a gas giant's orbit.
Armor:
Regenerating shields paired with armor I think accomplish the same effect as a 'pass or reject' type armor scheme, but the way armor works could be adjusted so that if a shot strikes a fully armored location, it won't do damage unless it would penetrate a certain fraction (say 25%) of the armor stack. That is, if a location is fully armored with 4 layers of armor, it will reject all strength 1 hits; if it's fully armored with 8 layers of armor, it'll reject all strength 2 hits, and so on.