Inkling wasn't the only content provider who removed their in-app purchases at that time, and they're not the only one to knuckle under and pay Apple a commission. And neither move comes as a surprise, though is worth noting.
Back when Inkling wasn't selling digital textbooks from inside their app they were in solid company. Content providers as diverse as Netflix, Pandora, Amazon, and Nook Media chose long ago to avoid paying off Apple and accepted the loss in revenues that represented. Some like Pandora simply could not afford to give in to Apple's extortion, while for others like Amazon and Nook Media it didn't matter that they couldn't afford to pay Apple 30%; they sold more items than Apple's in-app purchasing system could handle.
And on the other end of the spectrum are a bunch of smaller content providers that decided that they couldn't afford not to pay off Apple. This includes publisher branded content efforts like Sesame Street as well as smaller ebookstores like Izneo and comiXology. Even Kno sells textbooks from their iOS app, and that might provide a hint as to why Inkling changed their mind on this issue.
Not selling textbooks inside the app was probably costing Inkling revenue, which is never a good thing. But it is doubly bad for Inkling because like Kno, the Inkling iOS app is probably the single most common way that students access the textbooks bought via Inkling. That means that Inkling was hobbling their best sales channel. This update is a sign that Inkling has decided that they decided that they would rather pay off Apple than loose out on the sales.
Both paying Apple and not paying Apple are valid choices with downsides and upsides, so I am not criticizing them for making the decision or flip-flopping. But I will note that Inkling is an excellent example of why one should never tie oneself to a single platform, now matter how pretty. One can end up in a position where one has to pay off the platform owner just to stay there.
P.S. The changelog for the update doesn't mention any other changes, and from what I can tell the rest of the app doesn't appear to have been changed. The reading mode, menus, etc all look like they did in the previous version of the app.