By what mechanism does penicillin resistance usually develop in Streptococcus pneumoniae?
I think your guess is quite spot-on. According to this scientific article I found online, They did a whole genome sequencing on penicillin-resistant Streptococcus pneumoniae and their conclusion was


  ....is mediated by a mosaic of genes encoding altered
  penicillin-binding proteins (PBPs). Nonetheless, S. pneumoniae has
  also developed non-PBP mechanisms implicated in penicillin resistance.


In clinical medical laboratory point of view, S. pneumoniae's AST is done with oxacillin instead of Penicillin because OXA gives better cut-off between Susceptible, Intermediate and Resistance. You may see a big zone of inhibition when you used PEN disk but that doesn't mean the isolate is susceptible to PEN. This may suggests that "hydrolysis of the antibiotic by a beta-lactamase" is less likely to be the main mechanism?