Yes, I like this idea. It would also take care of the thematic problem, in fact it would add to the thematic element I guess you could say.
What about a Chenjesu type of modification to the fusion bolt? I have two specific ideas in regard to that.
a). Like the Chenjesu missile, the fusion bolt will propagate as long as you hold down the fire key. Once you release it, it would explode (by explode, I mean it would burst into small fusion blasts in multiple directions, like the Chenjesu shrapnel) with a power or range in proportion to how long you held the key (up to a maximum that would be roughly equal to the Kohr-Ah FRIED), which would thus dispel a range of energies (which makes it different from Chenjesu). Rapid fire of the fusion bolt would roughly follow the way it is now. An additional modification to not make the Dreadnought overpowered would be to decrease its speed slightly, but that can be worked out later.
b.) Turn the Dreadnought into a Broodhome with fighers. So, the fusion bolts would release shrapnel with a set range and energy. Might be interesting, might not.
Either way, I think you're pretty limited on your options unless you're planning on designing an entirely new weapon, right? You could either make the range bigger on the fusion gun, make it more powerful or make it do a trick (perhaps fire from different angles at the same time). Hope those ideas help.