Targeting a chunk of floor
First: it depends, but probably not, but you can probably do it anyway.
The Malefactor designates "a large or smaller ... object" as taboo. A 5-foot section of the floor is not an individual object, so it could not be targeted. A door is a single object, so it could targetted (assuming it's not ridiculously large); it appears that this is the intended use of taboo-ing an object. That said, in all but the most immaculate of spaces, there's likely to be some debris that the Malefactor can target legally.
So: if the floor is literally a tiled floor or a hardwood floor or has a throw-rug, probably, but you can't target a 5-foot section of "the floor", but you can probably find something that works well enough anyway (even if it means you have to prepare by tossing a pebble into a choke point).
Passing through a square
Second: "Creatures that attempt to ... pass through the square occupied by a Taboo ... object" must make a Will save or be stunned. As I read it, it's pretty clear that a Will save is triggered if a creature attempts to exit the object/creature's square via any vector other than the one from which it entered the square, on the same turn in which it entered the square.
So, we've got a 5-foot wide choke point with a taboo pebble sitting in the middle of it. The party is on one side, lobbing arrows at mass of goblins on the other.
The bravest of the goblins tries to charge the party; when he tries to exit the choke point, he makes a will save. If he succeeds on the save, the charge continues as normal. If he fails the save, however, he is stunned in the square with the taboo stone. When he can next act, he can pick up his sword, take a 5-foot step up to the nearest party member, and swing with no penalty: he's not passing through the square, simply exiting it.
The cowardliest of the goblins starts to run up to the party, gets into the taboo stone's square, and realizes that he left his oven on. He turns around and flees with out difficulty: he hasn't tried to pass through the square, he just entered and left it through the same side.
After seeing the brave goblin get stunned in the square, an archer might walk up into the square and start shooting arrows at the party; again, no chance of stunning because she's not trying to pass through the square.
As for touching: I read that as referencing the object, not the square: "creatures that attempt to make a melee attack against a taboo creature or object, that attempt to touch a taboo creature or object, or that attempt to pass through the square occupied by a taboo creature or object".