It all depends on your objective and goals. As with everything moderation is key. A balanced program of squats, deads, pushing exercise (chest/pecs) and a pulling (back/delts) is best for oevrall muscle, bone and tendon health. Whether you do this via free weights, body weight, or machines is really not material.
Rippetoe style heavy free-weight squats, squats and more squats is not the be all and end all of resistance training. Personally, I got into heavy strength training with Rippetoe's books and videos - and, IMHO, he did a great service by educating people about the benefits of heavy (free weight) strength training using a very very simple ('KISS') type program (at a time when the focus was on machines and overly complicated routines). His routines are great for beginners - especially very young ones - hence why they are copied and 're-mixed' so much (like Stronglifts 5x5 and countless variations thereof).
And I would really not suggest heavy squats for improving grip strength - that would be a very inefficient way to train your hand grip.
http://www.bodyrecomposition.com/muscle-gain/squat-versus-le...
http://www.thedreamlounge.net/barbell-squat-worst-exercise/
http://ericcressey.com/newsletter91html
https://criticalmas.com/2012/06/i-no-longer-give-a-squat-abo...
http://community.myprotein.com/off-topic/28225-mark-rippetoe...
https://forums.t-nation.com/t/rippetoe-ripped-apart/191700/7