Nothing wrong with that...I'd have probably made the same choice. There's security in knowing that you're all set to go for the fall vs. you MUST pass 3 tough classes with a C for your latter choice, or you're not going anywhere.
One of the reasons why I picked TJU was they were a lot more kind to my prerequisites due to some sort of mathematical "fluke." For some reason, between the UC system, quarter units, and the unit requirement at TJU...12 qtr units of, say, ochem + lab amounted to only 2/3 of the year's worth of ochem on the quarter unit side. I even verified this with admissions in writing.
If you still want to go to TJU, see if you can get an exception for microbiology. It sounds like microbio was cross-listed from bio to engineering and the "engineering" prefix shows up on your transcript. Other than that, goodluck! Enjoy the summer.