You have three choices:

a) Get DNN 4 working on 3.5 (I don't see any problem here with altering web.config, why would you not want to do this?).

b) Upgrade to 5.1.0 (I recommend using 5.1.1 when it comes out).

c) Contact the module developer and see if if is possible to supply a module version that will be compatible. It probably won't be possible if the module developer has specifically used DNN 3.5 features (seems pretty likely).

d) Rebuild/alter code if you have the source version.

In all cases always back up!

Thanks both you for replies, Alex, the module developer is me  :), and when I get dnn work on 3.5 it adds some entries to webconfig, this is the reason for i wrote it. I  found a solution, I am using C# DNN Module Template now and setting its Target Framework to 3.5, it works in 2.0 and 3.5 versions now without touching the sites.