Courts don't prosecute; they adjudicate on cases brought before them.
Article 11 makes the terms of the treaty enforceable in the Swiss courts at the suit of the individual whose rights have been infringed by non-observance of the treaty; for example a footballer whose club won't release his registration without payment of a transfer fee even though he is out of contract.
The Swiss court could of course decline to apply the relevant law in the same was it could decline to apply any applicable law not deriving from the FMP treaty - but that's not a matter of sovereignty but of miscarriage of justice.
...and you have a 'Kippers (which is to say not entirely factual) view of the relationship between the EU and its member states. The ECJ has no army, nor even bailiffs.
Unpacking this:
EU law is enforceable in the courts of the member states; one of the (EU) treaty obligations is to make it so. That is accomplished by a provision in domestic law to that effect.
Where the meaning of EU law is
acte clair (the meaning is clear on its face), or
acte éclairé (the meaning has been clarified by ECJ caselaw), the domestic court will just get on and apply the EU law in question. Where it is neither, the domestic court will refer the question to the ECJ for determination of that issue; and, when it receives its answer, will then go on and apply it. If the losing party declines to obey, the winning party will use the procedures of the domestic court to enforce the decision.
This means that if I am a professional footballer whose English club refuses to release my registration even after I am out of contract, my remedy it to go to the English courts; after Bosman, it is
acte éclairé that I am a free agent.
None of this is novel; it was in 1974 (the year before the UK's first in/out referendum) that Alf made his comment about the "incoming tide" of (then) EEC law.
The Swiss are required by Article 11 to provide an individual domestic remedy in its courts for those entitled to rights under the treaty. Where the rights are matters of EU law, then the Swiss court is required to "take account of" prior ECJ caselaw, into which category the
Bosman ruling falls. In this context, "take account of" means follow unless there is very good reason why not.
Where there is ECJ caselaw subsequent to the treaty bearing upon its content, then the issue is referred to the joint committee set up under the FMP treaty to decide how it will be applied. AIUI where, within the EU, an issue would be referred to the ECJ, it is under the FMP treaty referred to the joint committee for determination; but then
it is applied/enforced by the Swiss courts in the same way as EU law is applied/enforced byu the domestic courts within the EU.
It is true that the Swiss could ignore their legal obligations; but my impression (albeit my Swiss ancestry is rather less recent than yours) is that they are pretty law-abiding...
