It all depends what you mean by "running a smallport on a bigport harness and ECU".
You need to match the ECU to the sensors and electrics. Especially the injectors and dizzy (they run different ignition pickups). So if you have a bare smallport engine and fit bigport ECU, injectors, dizzy and probably some other bits I've forgotten then yes it'll run fine. Maybe not optimally as the CR and intake are slightly different, but there won't be any big issues.
If on the other hand you have a full smallport minus ECU and loom and want to slap it together with some bigport gear you have in the shed then it wont work.
There's been a bunch of chat about this, so take some time to have more of a read around and things should become clearer.
Hen