Considering how much supplies can do (rebuilding fighter wings, repairing capital ships from 1% to 100% with a relatively small amount), i suggest upping the price on supplies to act as a bigger limiter to offset the whole "rocket up to the fleetpoint cap and then halt there" thing that happens. Right each supply unit is valued at around 5 credits, selling at 4 and buying at 6. Scuttling a hammerhead right now would leave you with 250 supplies worth around 1250 creds. An odyssey leaves supplies worth 3000. If the price of supplies is moved up to 30 per, things start to make a bit more sense with the scuttling of a hammerhead leaving you with with supplies worth 75% of the ship itself. A scuttled odyssey would net about 12% return on the cost of the ship. High tech stuff is worth less when scrapped, but that makes sense considering most of the price of high tech is in the way the materials are put together, taking them apart wouldn't yield as much use.
There's probably something else in the starfarer roadmap that accomplishes a similar objective, i thought i'd throw this out there anyway. It would make bigger ships harder to maintain due to the extra crew, adding some more cost and value to someone who can manage to keep them rolling around a system other than just buying it and then dealing with only very minor repair and maintenance costs as long as it isn't destroyed.
Oh, and the medusa is probably under-priced for a high tech destroyer.