会社がいいわけがない denies 会社がいい, which answers the question "What (do you think) is good?" It's saying it's the company that is good, not something else.
いい会社であるわけがない denies いい会社である. This concerns whether the subject, which is omitted but assumed to be already known to the listener, is a good company or not. As a stand-alone sentence (i.e. taken out of the subordinate clause) it would be something like this.
When the adjective いい is used predicatively, the sentence usually follows this pattern.
This means that it is B that is good about A. You assess several aspects of A and determine that B is good. A and B thus form the whole-part relationship your teacher tried to explain to you. 業績がいい sounds natural (even without 会社の) because 業績 can be understood as one of multiple aspects of a company. 会社がいい doesn't because there is no whole of which 会社 is a part in this context.
When the subject is turned into a topic with が replaced with は, it is felt to be contrasted to something else.
This implies B is good unlike something else that is not good. (That's of course when いい means "good.")
Not all adjectives are like that, of course. Let's take the following sentence as an example.
Before it was put into the subordinate clause, the statement it denies was 地球は丸い. Here the adjective describes a characteristic of something that is assumed to be known to the speaker (and therefore topicalized). The sentence doesn't necessarily feel contrastive despite は.
いい is not this kind of adjective. It's about your judgment or feelings. What you think is good (i.e. the subject) is part of the new information conveyed to the listener and this makes が neutral and は particularly contrastive when いい is used predicatively. You should accept the difference in usage from other adjectives as it is.
By the way, いい会社であるわけがない sounds a bit stiff. いい会社なわけがない (from いい会社だ) may sound more natural in conversation.