c++ class memory consumption

I'm not sure because I don't use Eclipse, but I think that you can add compiler options in the project settings > Nios II Application Properies, into the User flags line inside the Flags category.

To disable rtti, use the -fnortti flag. To disable exceptions, use the -fno-exception flag.

If your compiler uses C++11 by default (I don't remember when it became the default in GCC) it's possible it adds some additional code. I think C++11 automatically generates copy and move constructors when you define a custom destructor but I'm not sure. You can try and revert to an older standard with the -std=c++98 flag and see if it gets better.