Are there any Counter-Samaritan proofs or essays that anyone out there knows of, i.e. Torah-based proof as to the fallacy of their practices/beliefs?
Probably the biggest fallacy is based on the findings of the archeologist Yitzchak Magen who excavated Mt. Gerizzim for over 20 years. He discovered evidence that some sort of Samaritan temple was active during the Persian and Hellenistic eras there on the mountain. This fits in well with Jewish traditions about the existence of a Samaritan temple during said eras (see Megillat Taanit, 21st of Kislev; Chullin 6a; Antiquities of the Jews 11:8; and some believe that the Dead Sea Scroll labeled 4Q372-1, line 12 refers to this same temple (see here)) and directly contradicts Samaritan traditions about the place. According to Samaritan tradition, they - as the only members of Am Yisrael who remained loyal to the first location of the mishkan (tabernacle), Mt. Gerizzim - continued to worship in the mishkan until it was destroyed due to the sins of Israel sometime before the destruction of the Temple (they don't deny that a Temple in Yerushalayim existed, they just think it shouldn't have been built there in the first place. Never mind now why; there are a number of reasons). The supposed destruction of their tabernacle is recounted in their various chronicles. Here's the description from Sefer Hayamim (my translation):
"In the days of Hoshea ben Elah who ruled over eight of the tribes of Israel1 and in the days of the [Samaritan] high priest Akavyah and in the days of Chizkiyahu king of Judah the king of Assyria came to the city of Shomron, laid siege upon it for three years and exiled all who were in it and in its [neighboring] cities to the cities of Babylon, and afterwards came to the city of Shechem and gathered all of the elders of the congregation of the Children of Israel the guardians of the truth2 and they are the sons of Yosef ben Elazar the priest and the sons of Yosef were trustworthy in the chosen place Mt. Gerizzim, the house of God [beit E-l], and he [the king of Assyria] said to them: Rise and travel to Charan...the high priest Akavyah rose and took the holy vessels and buried them in the chosen place Mt. Gerizzim, the house of God and wrote in the book of his people (another possibility: the book that was with him; in Hebrew: ויכתב בספר עמו) the location that they were buried in...and they exited...in mourning..."...but we are to be blamed and for this, this predicament has befallen us and the LORD has exiled us from the seat near the hose of God Mt. Gerizzim, the house of God...and since then the LORD hid the holy tabernacle for 494 years."
The various chronicles continue to describe how not long after that, the Samaritans were able to return to Samaria and they continued to worship on Mt. Gerizzim but without a tabernacle, until this day.
As stated above, archeological evidence directly contradicts this. Although no ruins of an actual temple structure have been found yet (leading to the theory that perhaps the temple was actually really a tabernacle), there has been found other evidence that some kind of temple or temple-like site did exist there. For one, piles of kosher animal bones were found around the site - probably the remains of sacrifices. For another, many inscriptions were found, attesting to the existence of the temple. One inscription reads:
"הקריב יוסף [על] [אש]תו ועל בניו [לפני א]דני במקדש"
"Sacrificed Yosef [for] his [wi]fe and for his sons [before the L]ORD in the temple"
"זי הקרב דליה בר שמעון עלוהי ועל בנוהי אבנ[ה דה לד]כרן טב קדם אלהא באתרא דנה"
"This was sacrificed by Delayah son of Shimon for him and his sons [this] ston[e] [in] good [me]mory before God in this site"
For more on these inscriptions and others, see here.
Since these findings contradict their traditions, the Samaritans have chosen to ignore the findings, for admitting they exist would devastate their religion3, which is on the verge of dying anyway (it was only in recent decades that they began to convert outsiders to their religion - when they realized they had no other choice4).
Other fallacies would probably come down to quibbling over textual differences and the like.
2 One of the titles the Samaritans use to refer to themselves, particularly in old texts.
3 This I heard from the person who organized our tour to Mt. Gerizzim and the Samaritan neighborhood on the outskirts of Shechem. And see the end of this post as well.
4 As explained by Yosef Cohen, the deputy of the current high priest and the next in the line of succession.