The main problem IMX with the Chertsey diversions (Southampton services) is not so much the alternative route, but the appalling paths they get given. They speed through about as far as Barnes and then crawl along behind stoppers pretty much all the way to Byfleet.
Would it not be a better compromise (more people get inconvenienced, but less severely) to reduce the frequency of the 'regular' Staines lines services when engineering happens to give more clear runs for the diverted fasts? This could include for example turning the Readings and Windsors into 'dividers' at Staines to clear up 2 paths an hour over the part of the route just up from Staines (or if dividing is too problem-prone, reduce the frequency of each to hourly and run at maximum length), and reducing the frequency of the Weybridge stopper to one per hour (freeing up another path).
To compensate they could even stop some diverted main line services at e.g. Richmond and Staines; a steady journey at decent pace with a couple of extra stops is much better than continuously crawling along behind signals! Something like this sort of flighting:
xx00 diverted express service (fast Clapham to Woking)
xx03 diverted main line service (Clapham Staines)
xx06 diverted main line service (Clapham Richmond Staines)
xx09 Reading and/or Windsor
(stoppers on the Barnes-Twickenham section slot in here)
xx30 diverted express service (fast Clapham to Woking)
xx33 diverted main line service (Clapham Staines)
xx36 diverted main line service (Clapham Richmond Staines)
xx39 Reading and/or Windsor
(stoppers on the Barnes-Twickenham section slot in here)
Could this work?