The 1874 RLDS edition replaced the preposition into with to; the 1908 RLDS edition restored the original into. Either reading is possible, although the text generally favors into, as we can see from the following cases of “and came over (in)to the land of X”:
In the last example, the 1837 edition replaced the preposition into with in (see the discussion under that passage). Here in Alma 21:12, the critical text will maintain the original preposition, into.
Summary: Maintain in Alma 21:12 the preposition into, the reading of the earliest textual sources (“they departed and came over into the land of Middoni”).