Well, if the Fortune Cards are a total flop (I'm suspecting they might be, as I really don't see anyone I know using them), then they might no longer be in production by September, in which case yes, I imagine WotC would change their minds about requiring them for "lair assault." However, I think that they're trying to make this "lair assault" program into the source of demand for Fortune Card collectors.
With Magic: The Gathering (the most obvious parallel to Fortune Cards), cards have secondary market value because there is demand for them in "constructed" decks, mainly by people who want to play in tournaments. If you need certain cards in order to improve your chances of winning, you may be willing to pay some money to get those cards (assuming that you care about winning).
With Fortune Cards, there is currently no "winning" to motivate secondary market demand, and I'm guessing that this "lair assault" program is supposed to create that "winning" incentive (if I have the right, rare, powerful cards in my deck, I have a better chance of getting through this assault). Higher secondary market demand translates to higher primary market demand (if the "chase" cards are pricey enough in the secondary market, it could be worthwhile to buy random packs instead, in the hopes of getting the right cards).
Thus, I expect that WotC will NOT pull the plug on Fortune Cards before they give this "lair assault" program a try. I expect a huge push for this program at GenCon.
To be clear, I'm not really interested in the "lair assault" myself, but I think min-maxers will be. So, this has a chance of succeeding from a business perspective. Me, I tend to ignore Fortune Cards - I don't use them in my games and I don't plan to. But they might appeal to a certain player psychographic (the "Spike" type of player from Magic: The Gathering parlance).
I'd be bummed if they started focusing all of their new product development on "competitive" D&D players, but I haven't seen evidence of that yet, so I'm not too worried for now. Come September, we shall see.