Heritage England understand that something will be done with the site. There was an agreement reached back in 2012 wit the award of eth outline planning permission that was granted for Liverpool Waters. That included a residential are that maintained the history of the dock, with water in it, and that water actually being a feature/focal point. What has happened now though is that it has changed from what was agreed. A large part of their argument isn't DO NOT BUILD EVERTONS GROUND HERE, it is, "this isn't what was agreed, and given the choice between the two, we will only support the one we agreed to.
With RE Stonehenge, though I know its off topic, its not like they are going in to destroy artefacts... some fella said potentially 500,000 artefacts will be lost... There is no way of knowing how many it will be, but you only have to get so deep and there'll be nothing there anyway, as it will be 'virgin ground'. they will be doing a lot of work at the openings of the tunnel, but I doubt they will need to worry too much after that. The level of testing, laser scanning and traditional surveys that will take place for the tunnel to be built will probably make those areas of the site one of the most data rich available.
As it happens, I would rather we just took people off the roads rather than make them bigger to accommodate, but that's not likely....