You need to develop your own threat model. This is a common truism that anyone with physical access to your equipment, motivation and enough time will be able to undermine something. This doubles if this attacker is an administrator on the server.
And yes, everything that is in your code is read with administrator access. You can try smart tricks, such as encrypting or obfuscating a password stored in binary / JAR files, but this is an obstacle, not an absolute barrier.
Again, on the other hand, there are no absolute barriers to privacy, just more or less effective barriers. Regardless of your measures, regardless of the strength of your encryption and key management, with enough time and incentives, something will give way. Which brings us back to my first point: what is your threat model (which attacks do you want to defend against); how much are your protected assets; and to whom and what do you trust?
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