I recall of a story where a Rabbi during the time of the Tosafists who personally killed many Jewish children in order to save them being raised in the Christian faith.
Anyone know source? Additionally, why was this permitted?
This case is mentioned in the Beit Yosef (YD 157):
מעשה ברב אחד ששחט תינוקות הרבה בשעת השמד שירא שיעבירום על דת
It happened that one rabbi slaughtered many children in a time of persecution for he feared they would leave the religion
See there for discussion of other rabbis who disagreed and for each side's reasoning.
You’re definition is rather vauge, but perhaps it is the intention of the Kinah recited during Tisha Ba'av, which discuses this time period:
Kinah 22 (Ashkenaz)
אֲבָל אָזְרוּ גְּבוּרָה יְתֵרָה לַהֲלוֹם רֺאשׁ וְלִקְרוֹץ שֶׁדְרָה וְאֵלֵימוֹ דִּבְּרוּ בַּאֲמִירָה לֹא זָכִינוּ לְגַדֶּלְכֶם לְתּוֹרָה נַקְרִיבְכֶם כְּעוֹלָה וְהַקְטָרָה וְנִזְכֶּה עִמָּכֶם לְאוֹרָה הַצְּפוּנָה מֵעֵין כֺּל וַעֲלוּמָה אָרִיד בְּשִׂיחִי וְאָהִימָה וְקוֹל נְהִי אָרִימָה:
They nonetheless girded themselves in great strength... saying, we have not merited to educate you in Torah ways. Let us sacrifice you like the olah offering...
Rabbeinu Peretz (Haggahot on Sefer Mitzvot Katan 3) ruled for this to be completely legal.
אותם קדושים ששחטו עצמם שלא סמכ' דעתם לעמוד בנסיון קדושים גמורים הם וראי' משאול
The martyrs that have taken their own lives because they could not withstand the challenge, are very holy individuals indeed, and the proof is from King Saul.