There are a few points in this article that are worth discussing:
1. One of the problems of the law in Israel requiring every Jewish person to get married through the Orthodox Rabbanut is that many (most) of them are not committed to halacha. And some will end up divorced without giving a 'get'. This creates a problem that any subsequent children born to the divorcee are considered mamzerim in halacha.
One solution which I have heard (quoted in the name of an anonymous godol) is to use non-kosher witnesses for any wedding when the officiating Rabbi is concerned that the marriage will eventually be disolved without a get (which according to some means the majority of non-religious weddings). This theoretically solves the mamzer problem, but causes many other sins by both the couple (living together without a chuppa etc) and the Rabbi (dishonesty and not providing the service he was employed to provide).
Rav Bakshi-Doron (Techumin 25 p. 100) writes strongly against this custom.
So in fact, the Tzohar Rabbi was being both honest and trusting in insisting on only using kosher witnesses. (Even though I understand the emotional trauma this caused). For this reason, when I was a Rabbi I had a rule that the Chazan and I were the witnesses at every wedding we performed. In this way nobody was embarrassed or questioned about their observance. Of course, in Britain there are also witnesses for the civil documents, which can be signed by anyone, so the couple can give their friends a special part in the wedding ceremony. There is no equivalent 'kibud' in Israeli weddings.
2. In the article Hess writes about 'Gur' (the non kosher witness):
How absurd. Gur could have been a tax evader, an abusive employer, or even a rapist, but the rabbi didn’t care about any of that. He wouldn’t have bothered to ask about his character. A good Jew, one who is fit to be a witness, can only be someone who observes the Sabbath (in the Orthodox manner). A secular Jew, no matter if he is one of the righteous few, a talmid chacham, or a bona fide Jewish hero, is unfit. Women, by the way, even if they are Sabbath observers, are considered unfit to be witnesses from the outset, simply because they are women.Really? Who says that a tax evader, rapist or other criminal is a kosher witness for a ketuba? Unfortunately there is an assumption that if someone dresses the part they also follow all the rules. But it is clear that a thief may not be a witness. And witnesses should do teshuva from any sin before signing the form. Perhaps if we could somehow change the perception that Orthodox Jews are tolerant of theft, tax avoidance, abuse and rape, we could avoid a lot of chilul Hashem.
3. Rav Bakshi-Doron (ibid.) writes in conclusion:
The issue of Orthodox marriages, to our sorrow, is not only not desired by a large segment of society, but has become a symbol of thsoe who hate Torah. They have made it into a shovel to dig against everything holy, claiming religious coercion. The question remains: Is it not better to do away with the law forcing Orthodox marriage, in order that the concept be not degraded? The greatest degradation is that enormous pressure is brought on Dayanim and Rabbis to permit that which is forbidden, or to convert people who do not want to be Jewish. Also the issue of annulling marriages to avoid mamzering causes desecration of the Torah, when we rejoice at finding invalid marraiges this avoiding the problem of adultery (and mamzerim).
This was written 8 years ago. The hatred of Orthodox has only increased since then. The numbers of questionable conversions and dodgy marriages continues to increase daily. The halachic problems and chilul Hashem caused by forcing Orthodox marriages are surely greater than allowing people the option of a civil marriage.
If the government forced people to marry through the Orthodox Rabbinate, it must also force the Rabbinate to convert people for marriage (which is forbidden by the Shulchan Aruch). Allowing civil marriage will do away with insincere (and potentially invalid) conversions, and will greatly lessen chilul Hashem in Israel.
If it were up to me, I would advise the government (and the Rabbinate) to allow civil marriages. But in exchange, conversions and divorce should remain firmly in the hands of the Rabbinate, without political pressure. (As to the question of Agunot - that is for another post. But things are slowly improving there due to sensible use of government legislation).