Yes if you buy $1000 of merchandise, you will end up spending $900 and then you can buy prime with the $100 you saved. However, you have to buy the $1000 of merchandise first. In reality that $100 is eaten by sales tax since if you work at Amazon you are going to be in a state where they have tax nexus.
I'm torn. On the one hand, I applaud you for not treating $1,000 in merchandise as a given. On the other... this just feels like an entitlement argument. It is just $100 we are talking about. For benefits that, if you use them, are almost certainly worth more than that.
On one hand, $100 is small potatoes and employees shouldn't care that much.
On the other hand, people are often irrational and do care that much. Which makes it kind of weird that Amazon doesn't provide free Prime to their employees, because that $100 value (and what's their actual cost?) probably buys a lot more than $100 of employee satisfaction.
So while I certainly wouldn't say that Amazon is somehow mistreating their workers by not giving them this stuff, I do think it's kind of weird that they don't.