They are probably taking the hubs out to make life easier => taking them to a machine shop, to take care of the bolts.
Even so ... if they don't remove the complete knuckle you will have extra costs not initially mentioned, like.. bearings.
Then again.. you do want to pay for somebody else to do the job... i would leave it up to them to find the solution they feel comfortable going with.
Trouble is I don't think the garage know what they are doing.
That being said:
get the wrench you used on the bolts and cut away about half a meter off the end off it.
There is a reason cars get shipped with small ~30 cm wrenches.. the leverage is supposed to be enough to correctly install and uninstall the bolts.
Or even better, get a torque wrench.