Forcing a ship to have more internal space (for crew quarters and such) is only going to make 'death cubes' more attractive, as they are highly space efficient.
Any mechanics to lessen the impact of death cubes (or "death blobs") I think would need to focus on making a bigger surface area more attractive, as the primary draw (to my eyes) of a death blob is that its very small (relative) surface area allows it superior armor and shield concentration.
The most obvious thing to me (and I've brought it up in other topics) is that a smaller relative surface area means less heat energy gets radiated into space per unit of volume. So both the larger a ship is in scale, and the more blobby it is, the greater the percentage of their cost, mass, and surface real estate will have to be dedicated to radiators in order to remain at operating temperatures.
I think if heat has a significant effect on gameplay it will make a good balancing element for both blobby ships and massive ships. As a rule of thumb, the larger a ship gets the more it will have to spread out to remain efficient and avoid having to have its entire surface covered with radiators (which don't make great armor, kind of defeating the point of a blobship).
One possible side effect is that blobbier (and larger) ships might naturally tend towards armor tanking (since shields presumably produce significant heat, and to capitalize on their ability to stack armor very efficiently) while smaller ships which are more heat-efficient might tend towards shield-heavy defenses (as a bonus, smaller ships are easier to disengage with to allow time to recharge shields, and would be even quicker if they eschewed heavy armor for lighter (but more power-hungry) shields).