but I don't want to hook them up in parallel in any way because the resistances of the two batteries will certainly be different, and will then cause the batteries to discharge each other slowly.
Not exactly. It will cause whichever battery has a lower voltage to drain the battery with the higher voltage - until the voltage of both batteries is equal. Once the batteries achieve equal voltage (resistance), then no current flows either way.
If one battery has a higher self-discharge rate, then as it self-discharges, current will flow from the other battery to keep them equal. So, they will ultimately both drain together - but they don't "drain each other".
The main problem with tying a larger and smaller battery into a
full-time battery bank, is that one of them is going to do more work - both charging and discharging - than the other, and will wear out sooner.
There is no problem tying different size/type/whatever batteries while they are being charged with a
constant voltage type charger (such an an automotive/marine alternator/voltage regulator setup). I'd say that might be a good place for a lowbuck diode-type battery isolator. If the brake battery is always half a volt low - well, so what?
EDIT: On second thought - no, not a good idea. If the house bank ever gets charged with a multi-stage charger, then the diode isolator is going to transfer that to the little brake battery, and it'll get boiled.
Probably have to rig a split-charge relay instead, but the problem would be switching it on only when the ignition is on...