There can't be physical "safeguards"; radio waves simply do not care about human borders.
There should be political safeguards, but these would require the regulatory bodies of two countries to cooperate. If cooperation fails, you get a political problem (not a technically solvable one, typically). If cooperation on a regulatory level between countries fails, the least they're probably going to worry about the constitution of some international organization that is occupied with coordinating a hobby internationally.
Personally, how would you even keep active repeater frequencies secret? It would take a person with an SDR transceiver seconds to scan all bands in question and minutes to figure out which frequencies get transposed to others. Keeping frequencies secret sounds more like a military thing to do (where you can actually make it illegal / punishable by localization and potential military counteraction to "probe" these frequencies) than something applicable to civil-access frequencies.
Extended Answer (from the comments)
Legally, nothing binds nations but international law (which not all countries feel bound by), only enforcable by action of the UN – and I'd assume it'll take a couple of decades to even reach a decision, and enforcement could typically only happen by means of violence; I doubt a halfway reasonable congregation of states will ever wage war because of IARU violations. So, no, there's no "realistic" legal ways to enforce things between non-cooperating states
Things look very different when states still feel bound by contracts they signed. But if tensions are high, like let's say between Pakistan and India, this commitment to contracts breaks down. Again, there's nothing legally binding states if states don't want to commit to that. International law very much is extremely only defined by the notion that it's
- better for all if states adhere to that; and
- the relatively abstract assumption that violation of it can have
embargoes or war as consequence. Again, states won't wage war
because amateur radio rights are broken, realistically.
So, the legal safeguard you can get can only work if the worst case – war with a neighbor – is actually so unlikely that neither side risks that. If, like you say, "tensions are high", then your best bet at getting a legal safeguard for the neighboring country not violating your rights is to make your own government find peace with its neighbors, and reinstantiate the rule of law on a basis of agreement. Sorry. There's no easier alternative.