‘[Prophet Samuel] went every year to Beth-El, and Gilgal, and Mitzpeh… and returned to Ramah… and he built there an altar unto the Lord.’ 1Samuel7
A major prophet, a highly respected authority on Judaism, doing what? Building altars! And he is not alone: Joshua, Manoach, David, Ezra, many other figures engaged in that absolutely prohibited activity. Rabbis have good explanations for each case, but if we look at the text’s plain meaning, neither the actors nor the authors had any qualms about unauthorized altar-building. It looks like the authors of the books of Joshua, Samuel, and Chronicles did not know about the Torah’s ban on out-of-the-Temple sacrifices.
After the Philistines released the Ark, it dwelt in several Jewish villages. Not even prophet Samuel thought of moving it to the official site of worship in Shiloh. The evidence suggests that religious service was not yet centralized.
History shows how problematic such centralization would have been. Left without God’s altars, Jews immediately lapsed into idolatry. The desire to have a nearby place of worship is deeply ingrained in humans. The legend that in the Second Temple period Jews refrained from idolatry is not exactly true. For one thing, transportation had greatly improved by that time, and the Jerusalem temple was not tremendously far away anymore. Nevertheless, archeologists have found many pagan worship items in Jewish settlements. Also, during that time synagogues began to appear, which allowed a venue for out-of-Temple worship.
The idea of a centralized cult was a great one: a truly abstract religion without daily contacts with divine proxies, be it altars or statues. The centralized religion was conceived to be unobtrusive, alowing people to go on with their lives without performing superstitious rites at every step. Unfortunately, that does not work, and so Jews are still kissing Torah scrolls and blowing kisses to mezuzas. The only expanding sect of Judaism for the past two centuries has been the Hassidim, a firebrand folk-style religion far removed from the cold and abstract Judaism of Leviticus.
We do not have the Temple. Never mind. It did not exist for most of our history in the Land of Israel. We do not have the Ark. Never mind. Prophet Samuel was not in hurry to get it from the villagers. The common law is clear: when there is no Temple, Jews are allowed to build altars and sacrifice on them. And this is our current obligation.