Jewish law to be determined by non-Jews

I always thought Jewish law was determined by leading Jewish rabbis who spent many years immersed in the study of the Torah, Talmud and other holy texts. However, after reading about two court cases in Israel and in London, I am shocked by the absurdity of secular courts encroaching on religious realms and having the audacity to determine what is halachically acceptable. I am quite nervous about these new developments. Will I be able to walk into a restaurant in Israel which is under Rabbinate supervision and be assured that it is kosher according to the highest standards? Or, will the certificate be issued according to a non-Jew's interpretation of Jewish law?
A Haaretz article entitled "Court rules rabbinate can't deny kashrut certificate to Messianic Jew's bakery" by Tomer Zarchin states the following:
"Following a lengthy legal battle, the High Court of Justice on Monday ordered the Ashdod Rabbinate to grant kashrut certification to a local bakery owned by a Messianic Jew.
Justices Eliezer Rivlin, Yoram Danziger and Salim Joubran ruled that both the Ashdod Rabbinate and the Chief Rabbinate Council, which backed its decision, had exceeded the authority granted them by the Kashrut Law when they demanded that the bakery meet special conditions not demanded of other enterprises solely because the owner is a Messianic Jew."
http://www.haaretz.com/hasen/spages/1096627.html

One of the comments posted by a reader on the VIN website regarding the article is the following:
"There is a story concerning Rav Yehudah Leib Malbim ZT"L. A Jewish butcher in his city joined the Reform temple, and Malbim revoked the kashrus of his butcher store. The Jew went to the Austrian secular court and sued to get his kashrus back. The Austrians ordered the Malbim to return the kashrus approval to the butcher shop and to announce it in his shul. the Malbim said, "As you know, I revoked the kashrus certification from Ploni's butcher store because he openly violates the mitzvos, etc. However His Majesty the Kaiser Franz Josef yorum hodo, holds a different halachic opinion and according to His Majesty's kashrus the Ploni butcher store is kosher and all of you who rely on the Kaiser's halacha can eat from there."

UPDATE: "The Supreme Court granted Konforti's appeal and ordered the Rabbinate to pay her NIS 200,000 in legal fees. The judges wrote in their ruling that: "The Rabbinate's conduct indicates that as far as it is concerned only Jews can receive this much coveted kashrut certificate." They also ordered the Rabbinate to issue Konforti a certificate as long as she adheres to the usual requirements. "

http://www.ynetnews.com/articles/0,7340,L-3739148,00.html

A second article which caught my eye was about a court ruling in England regarding acceptance to a Jewish day school.
"Jewish schools may have to change admissions rules after the Appeal Court held that ethnic tests of Jewishness amount to racial discrimination. A London school, the JFS, rejected a boy whose mother's conversion to Judaism it did not recognise. Faith schools may discriminate on religious grounds but the Court of Appeal held that this involved a test of ethnicity - which is unlawful. The United Synagogue says this will have "a very serious effect". In future schools would need to adopt a test of religious practice and guidance would be issued on this - pending a successful appeal or change in the law. "
http://news.bbc.co.uk/2/hi/uk_news/education/8118828.stm