I did something similar with my 2.5 gallon. Actually, between the two 2.5s I have I have probably done a complete rescape about 3 times. I had no problems in one. I simply added substrate to it, and added plants, but did not move anything. A second time I did as you are planning moved everything around. I had some scuzzy white stuff form on the surface and the water was cloudy for about a week, but water changes and such seemed to work. A single betta lives in the tank and he seemed no worse for the wear. In the other tank I once added a terra cotta pot with soil in it and everything went nuts for about a month. Most of the plants had a lot of trouble and lost their leaves, but they came back and are doing very well now. And I had crazy algae for about a week. Nothing else was living in it at the time.