Excluding Courses from Transcript that Did not apply towards my Degree

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I think you meant to say "exclude" in your post but the auto-correct had other plans.
Unfortunately I do not think that will be possible to just simply omit or erase the courses/history on the transcript. It will contain everything. You can write an optional essay to the BSChool Adcom and explain the reason behind your low grades and argue that your GPA should be calculated differently. They may go for it.

Their main concern with the GPA is that it is a long-term commitment measurement. Will a student stick around for 4 years in undergrad and be able to stay focused, overcome difficulties, and temptations, and keep their eyes on the prize. If they can do it in undergrad, they will likely be committed in BSChool and likely will graduate and succeed without getting a bunch of C's (which is an F in BSchool).

As long as you can address the concerns in the optional essay and tie your application together to show that you have overcome those issues and indeed you are not jumping from job to job, and you have been able to show professional progress, and successful engagement in multiple areas (work, personal life, hobbies, etc), that should help.

You can also search for "low GPA success stories" on GMAT Club and see what helped other people and what they did to overcome their lower GPA's (by lower, I mean 2.8-3.2 in the US system).