Alonso wants a stronger and more complete squad, as there's no guarantee that any player will be injury-free next season. Therefore, Alonso must strive to retain Vazquez, as he is a reliable defensive player, which could also benefit Madrid if other players in the defense are unwell. And if Madrid can't retain Vazquez, they should at least find a more suitable replacement, whether that means bringing in an external player or training the current players.
Building the squad before the new season kicks off is mostly what Alonso seem to be doing at this point, apart from injury, fatigue is another reason these players will need a substitutes at some point because been fatigue can make these players even prone to injury because they will not be at their best when they are fatigued and underperform to the point they could risk been injured on the field of play. Madrid has a good defence even with the absence of vazquez only that it will affect them a while but they can get someone to fit in real quick because they have it.
Of course Xabi Alonso is trying his best for Real Madrid before starting the new season because the problem of Real Madrid club right now is their defense line but I am sure Xabi Alonso will soon fix the problem, yes you are right fatigue may be a factor why they did not play optimally in the world cup between clubs because this tournament took place after the La Liga season ended and they have not had time to rest but fortunately now Real Madrid players are back in shape so there is no shortage to start the next season with full ambition but yes Xabi Alonso does have to recruit reserve players who are as good as their regular players so Xabi can rotate players easily.