Ecu's will typically work down to around 6/7 volts perfectly for this very reason.
Have you had a set up, what you are describing sounds like ignition is way too far advanced, this will cause a slow starter and spitting in exhaust, will even try to kick back if bad enough.
The webber/alpha is ok but a bit tricky to get into, there are better ecu's though, most ecu's will work on these tb's.
It will/should be ok once set up, gon onto live settings if it has them(I don't know) and tweak the timing down a touch to see the difference.
tabetha