Note that Wero is a private initiative by European banks (EPI), so I don't think EU representatives have much influence on this besides not making the same mistake with their upcoming “digital euro” which hopefully will become a Wero competitor.
Yes and no. These types of infrastructure are usually operated as a public/private construction, where a private party is responsible for building out, operating and maintaining the system, but the approval for (and tolerance of the power held by) that system is subject to strict regulations and performance expectations from the relevant government(s). This is doubly true for financial infrastructure. So although the system is operated privately, it is absolutely within the power of the EU to make demands of it, as they would with any other operational problems that threaten important civil infrastructure. Not complying with those demands could then lead to Wero losing the relevant licenses.
Some notable examples in recent times from the Netherlands are the drinks container deposit system (operated by a private consortium called Verpact, overseen by the government, and recently told to Do Better Or Else), and the situation around immigrant workers in meatpacking, where a minister openly told the industry that unless they fix their worker abuses in their self-regulation, immigrant workers in meatpacking would be banned entirely - and they followed through on the ban.
So yes, you absolutely should reach out to your political representatives, and ask them to look into this and/or enforce on it. They definitely have the power to do so.