Does this comma affect the meaning of the sentence?

Do both of these sentences imply two different ideas?

"I thought that the front room needed a bit of work but the rest of the house looked great."

"I thought that the front room needed a bit of work, but the rest of the house looked great."

While these are two independent clauses and therefore should be separated by a comma, doesn't the comma imply too much of a separation between the second clause and "I thought"? Both the clauses are the speaker's opinion and should both apply to the verb "thought." I'm unsure whether to take out the comma or leave it in.