Etz Yosef on the midrash writes:
"...וקאמר חבל לספינה כו' משום דכי היכי דספינה דאזלא בלא מכסא כל הסחורה שבה נתפסת בשביל העברת המכס. כך הוא בדינה של גיהנם כל גופו של אדם נתפס בה בשביל ערלה שלו. דכל מי שהוא נמול אברהם מציל אותו מן הגיהנם. וגם בג"ע אין מניחין מי שהוא ערל..."
Translation: "And what it is said that it's unfortunate that the ship etc for whenever a ship sails without a cover all of the merchandise is taken by the customs. So it is in the law of Gehinnom, the entire body of man is caught in it only for his foreskin. For whoever is circumcised [like] Abraham [it] saves him from Gehinnom. And also in the Garden of Eden they do not leave he who is uncircumcised..."
According to Etz Yosef, the sages weren't troubled that he wasn't Jewish, they were worried that despite his great act he would not receive his due reward because they thought he was uncircumcised.
Matnot Kehunah, on the other hands, writes:
"כלומר הצדיק הזה לא מל. אינו מדברי הספר אלא פירוש נכתב בתוכו."
Translation: "Meaning, this righteous man wasn't circumcised. This is not part of the words of the book but a commentary written inside."
Meaning that in his view, this bit was added in by a later commentator and wasn't part of the original midrash.
Dr. Yosef Yitzchak Kovok in Talpiyot notes on the Matnot Kehunah:
"...גם נראה שכל הספור במדרש מאוחר הוא...ואם מדרש ישן היה צריך לומר "ועליו נאמר" לא "וקראו עליו רבותינו"...וכבר הרגיש בעל "מתנות כהונה" בזה, אבל הוא רק על הפירוש "כלומר הצדיק הזה לא מל" אמר שאינו מדברי הספר..."
Translation: "...and it also appears that the entire story in the midrash is late...and were it an old midrash it should have been said "and on him it is said" not "and our sages said on him"...and sensed this already the author of "Matnot Kehunah", although only on the meaning of "Meaning, this righteous man wasn't circumcised" he said that this is not part of the words of the book..."