If you read the BBC article on this, they say "Sage did say the choice of scenario was significantly less important than maintaining other ways of controlling coronavirus - such as social distancing and hand washing."
I'm no fan of this government or the way they've handled this, but I'm not sure it's entirely fair to say that the government choosing to have year R, 1 and 6 go back first, instead of all children on alternate weeks, means they weren't "following the science". I'd imagine they went with a combination that was a good balance between science based risk analysis, and practicality.