O.k., so apparently you have booked your flights and are stuck with Greece and the dates and whatever weather and water temperatures you are going to get. Well then, why not make the best of it?
I guess the issue is, deciding what we want to do. I think she wanted
more options.
More options than what? Greece has about a million islands... What is she looking for?
Nothing has jumped out at us except for the Samaria Gorge and
Santorini.
Excuse me for being a bit blunt about this, but have you looked at any guide books at all? Crete is an island I have not been to (too big for my personal taste), but the very first information I find even on basic platforms like Wikivoyage is that the Samaria Gorge isn't open before May. I must admit that I am a bit surprised that this apparently came as such a surprise.
Again, make the best of it! If you are into hiking, have you looked at the European Long Distance Path E4 which passes through Crete?
And if Santorini jumped out at you, what is making you hesitate now? Santorini is gorgeous, especially for first-time Greece visitors and honeymooners and during off-season, so I really see no reason to overthrow that decision.
The main concern is if people think that Santorini/Island hoping would
be worth the trip in April over another destination. Janet mentioned
it was rushed.
That depends on how many islands you are planning to do. I think you could easily do Santorini and Crete (a small part of Crete only, obviously), but I'd hesitate to add another island to your itinerary. That would take two travel days from your twelve days of vacation and leave you with hardly more than three days per island.