Actually that's what I typically do in Java. There's far too much magic in Spring. Initialization code to read a parameter file and inject values into objects only takes a couple hundred lines. Plus there's huge value in controlling boot and exit sequences directly.

I do the same with object-relational mapping--write a thin layer of classes to wrap INSERT, SELECT, UPDATE, DELETE. Not hard to write, easy to test, and you can always slip into SQL if you run into problems.

Use-case specific code should always be considered as an alternative to general frameworks.