The Japanese Blu-rays of Stand Alone Complex (and the compilation movies) are 1080i, and that's probably what it's going to be on all releases (granted that they ever allow any foreign BDs of it, which is far from certain from the looks of it...) unless the distributors start messing around with it afterwards, which I hope they don't. The opening of the first season was animated at 30fps so that would get messed up in a 1080p version for one.
From what I've seen the pulldown is also very clean and a decent video processor shouldn't have much trouble with IVTC'ing it on the fly, i.e. the 1080i really isn't much of an issue. If they decide to IVTC it for the encode however, you will be stuck with any possible de-interlacing artifacts in the stream, even if your own video processor may have handled those sections better.
One curiosity in all this is that the PAL DVD master actually was progressive, sped up from 24 to 25fps. I'm not sure if this was thanks to Manga/Madman or Production IG, but unless I'm mistaken it did mess up the opening, either through blended or dropped frames.