You can cut it back quite severely (you can lop more than half off and it will be fine) - you can use the branches as cuttings and make more plants. It will overwinter in the house although you should watch carefully for spider mites and aphids.

The leaves don't grow in pairs which are close together. It's probably behaving just as it should. If you think, however, that it's leaning towards the sun, you have a good indication that it needs more sun.

Pineapple sage can deal with quite savage pruning - necessary in a warm/hot climate - but since yours is such a baby, and you're in a cool/cold climate, I would leave it alone for now. You want it to flower, don't you?