Although generally all offerings had to be brought on the central holy altar in the tabernacle, so long as the Nation was unsettled, the use of other altars was permitted. The main difference between these altars was that while the altar in the tabernacle was carefully secluded from anything profane, the local altars had no such restriction. As such, the offerings brought upon them would bring down Heavenly influx directly to all the nations, not only through the medium of Israel, for the Divine Presence was still in exile during this period. So long as the nation was struggling to attain their position as rightful owners of the Holy Land, they continued to support the nations in it, as Hashem promised them - "you will not be able to cast them out right away, lest the beasts of the wild (human frailty) overcome you".
When a person is still limited to a dimension that is base in relation to the level he is striving for, he need not shake off his relationship to that level before attaining a strong foothold in the next, for the positive energy employed in changing neutralizes negative elements in the environment. Only when he reaches a state of relative stability in his new attainment must he re-examine his surroundings and eradicate influences that were not detrimental while the positive change was in motion. Its like climbing a ladder — for one foot to be free to move up, the other one must be on something steady.
Unfortunately, even after our forefathers reached full independence, and the Divine Presence found it's rightfull resting-place, they did not eradicate that human frailty and the altars stayed around even in the days of the righteous kings. Eventually, this strengthened the surrounding nations sufficiently to overcome us and send us into exile. If in our exile however, we continue to strive diligently, the negative influence of altars on foreign soil will not hinder our growth. By nurturing the Divine Presence which joined us in our exile, we can bring It back to our Holy Land and preserve It in complete holiness in our midst.
Based on Rabbi Vali's book on Dvarim. Questions and subscriptions can be mailed to: the Yeshiva