So in my opinion we wouldn't want to replace the affiliation strings, just attach an affiliation as well, right? I.e. in addition to the qualifier:
P6424 "School of Pharmacy and Medical Sciences; University of South Australia; Adelaide Australia"
add an additional qualifier:
P1416 Q64092240
Or would we prefer the more general university-level affiliation: Q15576 ? Either way we will lose a bit of information (and with the second option more) if we replace the affiliation string rather than just adding another qualifier...

When converting from string to item, we could go for something like P1932 (stated as) that would keep the string attached to the structured statement and would allow conversion to something more granular later on.