Dairyground,
For ATC it is a balancing act.
On the one hand you shouldn't have too many departures started and taxying out for the reasons you mention (taxi time, noise, emissions, waste of fuel etc).
On the other hand, at a capacity constrained airport like LHR, we need to get aircraft off the gates to allow inbounds to park, and to make best use of the runway capacity, the departures controller needs a handful of aircraft at teh runway holding point to ensure a good mix of traffic (i.e. left, right and 'straight aheads' which, if traffic flying in one direction is followed by traffic going in another, can all depart 1 minute apart). The very worst thing we can do is to be delaying aircraft on stand and there to be wasted capacity at the departure runway.
Same reasoning exists inbound, to ensure that no capacity is wasted on the arrival runway, and to ensure that Heathrow Approach have a selection of traffic to get the best order for landing, if there are delays then we try to have a few aircraft holding in the stacks.
As to holding on the ground instead of picking up long delays at the destination airport, this occurs already. However, given all the variables, it is a very blunt tool. The already referred-to CDM will help in making the predicted airborne time far more accurate than before, which allows for more accurate traffic forecasts, which allow for fewer restrictions being in place.