All tanks with filters can be cycled, it's just a matter of how long it takes and what method is best to use for what tank. Cycling is not something we aquarists do, it's something that happens naturally. What we refer to as "cycling" is really just us aquarists trying to speed up a natural process called the nitrogen cycle. So, don't worry, your 2.5g will cycle. I think when people say 2.5g tanks can't cycle, they mean they don't cycle well with fish in them because you have to change the water so frequently. But a fishless cycle should work.
As for the gravel, I don't see why you couldn't quickly remove it, rearrange the plants, and replace it. If you want to remove the gravel completely, it might slow the cycle down a little but not significantly. The main thing is to continue using the shrimp or fish food to keep the ammonia level up. Once the nitrites start appearing, you've reached the second stage of cycling.