Is it lesphobic? Yeah probably but its the least problematic for this manga when the main girl is still "???" on her own sexuality. The assumption of thinking the mangaka hates lesbians reminds me of how society tends to think yaoi is made for straight women when they are queer afab.
Besides, Watsuki is literally still getting money from Rurouni Kenshin. Mangadex still has upload translations of the manga Galko-chan when both mangakas were arrested for CSAM. Pretty sure that is waaaay worse and to get angry about