When reading the article I do get the impression they try to downplay the potential risks.

quote 1: “These puberty-pausing medications are widely used in many different populations and safely so,” McNamara says.

quote 2: “From an ethical and a legal perspective, this is a benign medication,” Giordano says. She is puzzled by the extra scrutiny these treatments receive, considering their benefits and limited risks. “There are no sound clinical, ethical or legal reasons for denying them to those in need,” she says.

quote 3: Like any medication, GnRHas carry the potential for adverse effects.

Now if you read one of the studies they link (https://pmc.ncbi.nlm.nih.gov/articles/PMC7497424/).

quote: "Arguments against the use of GnRHa that have been raised include possible long-term adverse effects on health, psychological, and sexual functioning (Laidlaw, Cretella, & Donovan, 2019; Richards, Maxwell, & McCune, 2019; Vrouenraets et al., 2015)."

I really feel like they overstate the strength of their positions with the articles they cite. All of them show clear limitations of the results which clearly show we need more data.

I don't think Scientific American are exactly hiding that they hold a position on the issue. But I don't think that they've misrepresented that study, which is an observational study looking for evidence of whether there's any truth to those sorts of arguments (the citations appears to be two letters to the editor and an ethics paper...) which didn't find them, mainly because there weren't many dropouts to study.