We have cannons to kill monsters, more reliable than stone throwers in that role, therefore the fact that mortars are worse vs multiwould creatures is not that important. Most O&G use stone throwers and find them worth the points as far as I know, but then again they are used for sniping a lot. Our mortars are really only useful vs T3 enemies or in combination with shadow magic. That is a pro for S3 with D6 under hole, vs higher toughness enemies and for sniping.
Vs smaller units, yes, ordinary stone throwers does more damage, but only if you roll a HIT, a big template has a bigger chance to at least hit some models. Therefore I think the two are somewhat comparable in that regard.
Mortar has armour piercing rule which is really nice, ordinary stone throwers does not have any modifier to armour at all. Plus for mortar.
Black powder misfire chart is worse, another negative factor for mortar.
Overall I find that rock lobber and mortar are about equal, mostly because we have cannons for sniping monsters. Therefore a cost of about 85pts would be fine for mortars, from 75pts up to 90 max is acceptable. Now I find it strange that other armies, which rely on close combat have just as good or better template weapons as the Empire, which is our strength now?