To be honest, if your application adds value that is obvious to a company's leadership [and that's the goal with B2B sales] then nobody will care that it uses the JVM. By which I mean both that the leadership won't care and that the nobodies in IT who might care will be given marching orders regardless of any animosity.
The bigger hang up I see with the JVM is for companies that are .NET based. As with the previous paragraph, that's a market analysis question not a technology one.
Finally, the security threats to a mostly offline application designed to communicate with a central server are relatively low in comparison to something based on constant internet connection and web technology. Of course, as always, the people designing a system for the JVM need to know what they are doing.
In a market where desktop applications make sense, selecting a language that facilitates use on both the JVM and .NET might be a consideration. That's not to rule out targeting the browser, it's all tradeoffs.
Good luck.