Can the word Gentoo be used in a derogatory way?

As far as I came through didn't found portuguese Gentio from which the English Term Gentoo originated to be derogatory but the parent word gentilis from late Latin has some concerns.

Here is a brief etymology of the word Gentoo.

Gentoo [archaic] | Gentoos [plural] First use: 1638 Origin: Portuguese gentio, literally, gentile, from Late Latin gentilis

Gentoo [archaic] Origin: Portuguese gentio, heathen, gentile from Latin gentilis: see "gentile"

Gentoo [sometimes not capital, archaic] | Gentoos [plural] First use: 17th century Origin: from Portuguese gentio pagan (literally: Gentile)

gentoo | gentoo penguin First use: mid 19th century Origin: perhaps from Anglo-Indian Gentoo "a Hindu", from Portuguese gentio "gentile"

gentoo | gentoos [plural] Origin: Of Anglo-Indian origin (17th century), apparently a corrupted form of gentile ("pagan").

Also, do consider this link for usage examples in various media and articles.

Abhijeet as your name suggests, you are from India thereof a personal answer is that though in English and other foreign languages the Gentoo may have different meanings but as far as Indian meaning goes, the word is often used in a combination: jeev-jantu which offcourse would be something which can be teased by naughty fellow mates.