We are taught the kashrut mitzvot are meant to elevate our holiness and avoid spiritual contamination. What of an uneducated Jew that for most of his/her life did not keep kosher and eventually became aware of its importance? Can that spiritual contamination be reversed by committing to the laws of kashrut later in life or is that contamination irreversible?
This whole concept points back to Lev. 11:43:
אַל-תְּשַׁקְּצוּ, אֶת-נַפְשֹׁתֵיכֶם, בְּכָל-הַשֶּׁרֶץ, הַשֹּׁרֵץ; וְלֹא תִטַּמְּאוּ בָּהֶם, וְנִטְמֵתֶם בָּם.
"Don't eat any of these creepy-crawlies ... you will become impure due to them." The word venitmeitem is spelled missing an alef.
The simple reading is that it's the same, tamei. From a strict halachic perspective, there are non-kosher foods that would make the eater tamei, however the person would become tahor simply by going to the mikveh and waiting till nightfall. And today we don't really care about this kind of tamei anyhow; many of my best friends are on the chevra kadisha and handle corpses -- everyone's tamei in a halachic sense, and we don't really worry about it.
The question is trying to use "tumah" in a broader spiritual sense of "bad things." That connects with the midrashic reading of this same verse, that "venitmeitem" refers to timtum halev. Thus people have occasionally gotten spooked about the horrible spiritual effects of non-kosher food, and occasionally forgotten that we do mitzvos because God commanded them. And God also says there is such thing as repentance, and also such thing as nullification! (If one drop of Campbell's chicken soup falls into a hundred gallons of water, the water is kosher. If halacha -- i.e. the will of God -- says it is kosher, then you don't have to -- and in fact, should not -- worry about it messing up your soul!)
With that lesson in mind, in essence your question does in fact therefore translate into the question about timtum halev, and the answer there said it best: if in Temple times it could be repaired with a standard animal sacrifice, then repentance is the medicine here.