My kids both went to Thomas's Clapham and loved it and went on to extremely good secondary schools, as did all their friends, so I'm a little puzzled by your academic concerns (although I may be out of date). I agree with the points above, particularly those made by Dudette and Medicalmam.
I would add that my experience of Thomas's, which would probably be the same for any energetic fee-paying junior school (post Covid), is that you would be unrealistic to think that you/your partner would just be doing two trips to school a day, particularly when your second child joins too. There were before-school clubs (music, drama, sports), assemblies to watch, after-school clubs of all descriptions, lunch-time concerts and dance shows for parents, Saturday gymnastics and sports fixtures, Parents' Evenings and all sorts of talks and social events in the evenings. Nothing compulsory, just really nice to get involved with - but thank goodness we lived ten minutes walk away! Your daughter(s) might not want to take up all those opportunities, however it would be a shame to deprive her of those she would like to do or not be able to watch/support her because the commute is too much or the logistics impossible.
I also would point out that Thomas's is opening it's own senior school in September, which should be reasonably well-established by the time your eldest gets to that point and is likely to be a high quality and sought-after school once it takes off. So if 11+ exams feel too much or as a fall-back to take the pressure off, then there will be that option not to have to change schools if you did go down the Thomas's route.
Good luck with the decision.