"the growth of membership on Safari far exceeds the individual units previously purchased on oreilly.com"
... that doesn't explain why the two options couldn't co-exist.
"In addition to giving our customers the choice and convenience they expect"
... no, they just took away the choice and convenience I expect.
Over time, I've favored different formats based on what devices I have owned, and bugs in the apps themselves (OS X 10.11 Preview had terrible PDF rendering for non-retina devices). So there goes my choice on what I want to buy when, and what format to use where.
I hope this doesn't encourage InformIT, Manning, PragProg or RockyNook to go down these roads. Until then, I guess they will get my money.