Here's the list of requirement for core biochem:
http://registrar.mcmaster.ca /CALEN...nt/pg1513.html
2EE3 is an antirequisite for 3D03, and 3G03 is an antirequisite for 2B03/2BB3. You won't learn the material nearly as in depth as 2B03/2BB3, but if the advisor told you that taking these courses will let you get around the 2B03/2BB3/3D03 requirements, then it's probably okay.
2EE3 + 3G03 often substitute for courses requiring 3D03 or 2BB3, so you should be alright taking upper year courses if you only take 2EE3 and 3G03.
What program are you going into instead? Molecular Bio & Genetics people are allowed to take 2B03/2BB3, but I don't know if that program is an option for you. Alternatively, you could beg the program advisor to waive the prereqs and let you take 2B03/2BB3.