Dual intent is applicable in such a case, but of course they may decide your son is not likely to leave at the end of the study permit. In that case (a refusal), you could request a TRP on H&C grounds to overcome their finding of inadmissibility - it's not guaranteed, but as you point out the extended delay in processing your application (3 years and counting) is not your fault and it is not good for your child, either.
If you have a NOC B LMO, have you considered applying for AEO FSW track? Or maybe even PNP track? If you qualify, those are both independent of spousal and do not require that you do anything with your spousal application.