Putting him in 5th or 6th would not be penalizing him for switching to a safer tire. That position was where he was when the red came out. Do you think drivers should not lose spots when they choose to go on to inters or wets?
Drivers like Alonso didn't pit because they thought it would get red flagged and they would therefore lose out by pitting, even though it was the safer (and probably faster) tire. Where possible, they shouldn't be penalising pitting for a safer tire. The 1 sector lookback gives a little protection to drivers that do pit - but there was some discussion on if Perez would end up restarting at the back because he got stuck in the pit lane - that for example would have been a stupid penalty on safety
I'll never understand why they can count minisectors when it suits them but then randomly say "we have no way to determine the racing order" on a red flag.