"Your ignorance is breathtaking."
Hm. That's never a good start.
"Trans people are in fact the gender they identify with because their brains are biologically the same structurally and metabolically as those of the gender they identify with."
Are we talking about gender or sex? If you're a transwoman and you want to claim ownership of a woman's brain, there cannot be a debate about that, because "woman" is an gender identification. I can't run an experiment to prove or disprove anyone's gender identification.
However, if you want to claim ownership of a FEMALE brain, which changing the topic from gender to sex, there's no way to debate that either; there are indeed differences between the male and female brains, but there's no way to confirm which you have short of an autopsy, which I assume you're not volunteering for. :-)
I believe the point the OP is attempting to make that SEX (not gender) is not alterable, which is correct. About 99.87% of all humans are born with the sexual organs to produce one of two gametes; simply put, you were born with the organs to produce either an egg or a sperm. HRT doesn't change that; nor do any interesting surgeries that may be developed in the future. And should future generations dig up your decomposed body in a few hundred years and examine your skeleton, they will conclude you are male, regardless of what miracles modern surgery can do to you. The angle of articulation between femur and pelvis, and the shape of the pelvis, is a dead (pun intended) giveaway.
These are all facts. So, the larger question is "does any of that matter, as far as society is concerned?" The answer, of course, is NO, it doesn't. There's no reason why, legally, professionally, socially, etc., a person cannot live their life in the gender role they choose. But at the same time, there's no reason why we have to play around with language and be obtuse about the meaning of words. The now-popular phrase "Transwomen are women" can be true legally, professionally, socially......but it's not true medically or biologically. Transwomen past the age 50 will still need their prostate glands checked for cancer.
"I try to be generous and understanding when people make the kinds of comments you did in your article."
Well, you weren't. You were condescending and snarky. :-)
"I have spent my life in ministry, and I understand and accept transgender people as part of G-d’s greater plan."
Not sure "plan" is the right word, but in Islam, transgenderism has been accepted as an existing human condition by both the Sunni and Shia since the early 1990's. And as religious people, we move forward from that position and do our best to quash the bigotries and misconceptions that arise therein. Best way to do that is to avoid namecalling, and certainly to make sure we are very specific about separating sex-based statements from gender-based statements.