Perhaps make it that all heat sinks in the engine are single only and if you want doubles they are mounted outside the engine.
Cray had an idea where you develop half-mass heat sinks. Clan versions take up half a ton, 1 crit space, and dissipate 1 pt of heat. Engines can still only mount 10 heat sinks. Effectively they are identical in heat dissipated per ton and critical space as regular DHS, but are more resistant to damage.
Inner sphere version might be half a ton, 2 crits, and dissipate 1 pt of heat.
Disadvantage is you lose the 10 extra heat being dissipated by the engine. Advantage is your heat sinks are more robust (instead of a single crit taking out a DHS and removing 2 pts of heat dissipation, you only lose one of the two HMHS and 1 pt of heat dissipation).
Of course, I'd want to be able to mix half mass heat sinks with regular heat sinks, as the half mass heat sinks in the legs are not as heat efficient as regular heat sinks for their size.
Of course, I'd want to make Flamers and Inferno rounds to heat damage based on the number of heat sinks a target has. Perhaps a Flamer would do 1 pt of heat for every 10 heat sinks the target has (FRD, min 1 per attack), and Infernos would do 1 pt for every 20 heat sinks (and since Infernos are fired in salvos, this isn't as bad for the attacker). If multiple sources of heat are fired, they are totaled and divided, then rounded down. So a single Flamer against a mech with 15 heat dissipation would do 1 pt of heat, while a unit mounting 2 Flamers would do 3 pts of heat. A unit hitting with 5 Inferno SRMs would do 5 pts of heat, as the regular math would be 3 pts of heat (5 * 15 = 75, 75/80 = 3.75, FRD = 3), but since there wee 5 SRMs it will do 5 pts of heat.
This also means we need to make larger Flamers >:D. Imagine a 5 ton mech Flamer, fed off the main reactor, with the following stats:
Hvy Flamer:
Heat: 15
Dmg: .9* (Heat)
Range: 1/2/3
Tons: 5
Crits: 5
* Does 9 pts of heat for every 10 points of heat dissipation the target has in operation, minimum 1 pt of heat. If the target does not track heat, it does 4d6 damage (more than the little Flamer, but since it is a single weapon instead of smaller redundant).
* As anti-infantry, does 3* the damage of a regular Flamer as anti-infantry damage (not as efficient as the smaller, as it is still a single stream).