"He declared all food clean" was Jesus' concluding answer to those who disliked the fact that some of his disciples were eating without first washing their hands. This short clause is usually understood to mean that "by saying this, the Lord was abolishing all distinction between ceremonially clean and unclean foods" (Tyndale New Testament Commentaries on Mark 7:19).
This interpretation implies that Jesus abolished all those commandments concerned with pure and impure food and food utensils. For instance, it is used to explain that commandments such as "you shall not boil a young goat in its mother's milk" can now be ignored by Jesus' Jewish followers. Likewise, Jesus words are interpreted to mean that Jewish believers no longer need to pay attention to commandments like "any earthen vessel into which any of them [unclean animal] falls you shall break; and whatever is in it shall be unclean" (Lev. 11:33).
Mark, however, never imagined that in highlighting the controversy over ceremonial hand washing Jesus would be depicted as a Messiah who teaches to ignore the Law. This, for him, would be unthinkable, since the very Law Jesus submitted himself to says that a prophet shall be put to death should he "entice you from the way in which the LORD your God commanded you to walk" (Deut. 13:5). In other words, the interpretations of Tyndale and others like it are reducing Jesus to a false prophet.
Ceremonial hand-washing was a major issue for Hillel and Shammai, the two most important sages of the first century BC. Though based on Exodus 30:19-20, hand-washing was understood not as biblical, but rather as a rabbinic precept that was seen as equally binding in light of the command "according to the judgment which they tell you, you shall do" (Deut. 17:11). Important as it was, this rule was contested even by sages who lived a generation after Jesus: "But whom did they excommunicated? Eliezer the son of Enoch who demurred against the laws concerning the purifying of the hands" (Mishna, Eduiot, 5:6).
If anything, therefore, Jesus is contesting a rabbinic rule, not a biblical command. By so doing he is demonstrating a full awareness of the well-known distinction between "Pentateuchal law" and "Rabbinical law" – the first being more important. This does not mean that a Jew should ignore the rabbis, but it does mean a rabbinic rule can be contested, at least until it is accepted, a process that can take many years, even centuries.
The debate depicted by Mark therefore portrays Jesus not as someone who teaches abrogating the Pentateuchal dietary laws, but as one who challenges his rivals' neglect of the biblical law for the sake of rabbinic rule: "For laying aside the commandment of God, you hold the tradition of men" (Mark 7:8). While the Tyndale commentary wants to convince us that Jesus teaches the abolition of the Law, Mark is telling us that Jesus in fact reprimanded the religious leaders for abandoning it.
Though views of what exactly Jesus meant by saying that "only what come out of man defiles him" may vary, it cannot and shouldn't be denied that even in this case where he stands in sharp opposition to the elders, Jesus' sole intention was to make his opponents realize that they were in real danger of putting Rabbinic Law above the Pentateuchal.