1. Everyone has the right to freedom of thought, conscience and religion; this right includes freedom to change his religion or belief and freedom, either alone or in community with others and in public or private, and to manifest his religion or belief, in worship, teaching, practice and observance.

2. Freedom to manifest one's religion or beliefs shall be subject only to such limitations as are prescribed by law and are necessary in a democratic society in the interests of public safety, for the protection of public order, health or morals, or for the protection of the rights and freedoms of others.

Building minarets is clearly not contrary to the rights and freedoms of others, so it'll only be allowed by the ECtHR if they think it's necessary for public safety (unlikely), public order (which I think is put at more risk by the ban than by minarets), public health (only a problem if they start blasting out the call to prayer at 5am – an entirely different issue) or public morals. Public morals is the only one that could possibly justify the ban, as it could mean pretty much anything!

Also, don't forget Article 14.

The enjoyment of the rights and freedoms set forth in this Convention shall be secured without discrimination on any ground such as sex, race, colour, language, religion, political or other opinion, national or social origin, association with a national minority, property, birth or other status.

In view of the above, I think it definitely is a human rights violation to have a law directed at a specific religion's peaceful practices without a very good reason. However, the ECtHR doesn't seem to have a great record on freedom of religion: they didn't seem to care about France, Switzerland and Turkey banning Muslim headscarves in educational establishments (see link).

The other important question is what legal effect a successful challenge in Strasbourg would actually have in Switzerland. From what I can work out, Switzerland has ratified the European Convention on Human Rights, which I believe means they've promised to try their best (unlike the UK, which has actually enshrined the ECHR in domestic law). So it might be quite hard for the Court to overturn a constitutional amendment.