They're not, Index is.
The games with S. Links are the most popular, best-selling games in the series, with the most merchandising and - after P4 - psudo franchise potential. S. Links and the calendar aren't going anywhere and don't need to. Growth and evolution == throwing out gameplay elements the team is consistently hailed for that generally work quite well. It means improving them.
I don't think it will even get as far as Index forcing them to do it. Hashino will be quite aware of how much people like S Links. Whenever Soejima and Hashino do interviews, friendship and bonds and all that are always a major part of it. Persona has become as much about the links between people as it has about concealing aspects of your personality.
S Links aren't going anywhere. The only possibility I can see is that they get re-jigged a little.