As is often the case, people assume because some sin-crime has such a punishment that it's permissable or commanded the punishment be meted out. WRONG!
Before you go executing someone for sin they get a trial first. And compared to our modern system, Jewish trials require a lot more in the way of evidence.
Just SOME of the judicial procedure commandments:
Not to appoint as a judge, a person who is not well versed in the laws of the Torah, even if he is expert in other branches of knowledge (Deut. 1:17)
Not to curse a judge (Ex. 22:27)
That one who possesses evidence shall testify in Court (Lev. 5:1)
Not to testify falsely (Ex. 20:13) That a witness, who has testified in a capital case, shall not lay down the law in that particular case (Num. 35:30)
That a transgressor shall not testify (Ex. 23:1)
That the court shall not accept the testimony of a close relative of the defendant in matters of capital punishment (Deut. 24:16)
Not to hear one of the parties to a suit in the absence of the other party (Ex. 23:1)
Not to decide a case on the evidence of a single witness (Deut. 19:15)
Not to render a decision on one's personal opinion, but only on the evidence of two witnesses, who saw what actually occurred (Ex. 23:7) Not to execute one guilty of a capital offense, before he has stood his trial (Num. 35:12)
Not to rebel against the orders of the Court (Deut. 17:11)
Also, being transsexual isn't a sin-crime. Crossdressing's mentioned, but only if the purpose is to mislead others into believing you're of the false-sex. Obviously then, a transsexual is known to be a transsexual and thus isn't being mistaken for a real woman.