That's not science. If I invent something that's (as close as possible) self-consistent but has absolutely no plausible empirical connection to modern science, then I have come up with a very well justified system of magic.
Is it not science if in a fictional universe certain things work differently from ours, but are understood according to scientific methodology? The problem of "space magic" exists not because it can't be science, but because the SF genre (most call it "speculative fiction" these days, which is more accurate IMO) generally assumes its universes are like ours in most ways. We retain an existential connection to SF universes because they could be interpreted, if not always as a possible future of our civilization exactly, at least as a possible future of a civilization very much like ours in a universe like ours. As long as that connection is maintained, the story stays convincingly within its genre, and that means that technology can get pretty fantastic (magical, if you want) as long as it only occupies unknown space in our body of scientific knowledge, and doesn't contradict it. Occupying that unknown space, however, means that new terminology is occasionally needed, even in the hardest of SF universes. After all, if it didn't have anything new, why call it SF?
In ME1, the whole plot is made possible by magic space telephones that beam images into your mind, and not one but two plot critical revelations are only possible because Asari can read the minds of other alien races, including one that is a [x] thousand year old plant.
Well....I guess you have a point here
I used to think that the Prothean beacons aren't that "magical" once FTL has been established, but any rationalization collapses once you start to think it through.