What do you think?

I start seeds in styrofoam cups. I do exclusively square foot gardening and have several boxes going. I use the 32oz cups that I buy in bulk from Sam's Club. I put about 1 inch of potting soil in the cup.
When it comes time to plant I just cut the bottom out of the cups and plant the whole things. This leaves me the proper amount of empty cup to do the watering called for in the Square Foot Gardening book.
Well, everything that happens, wilt, browning leaves, low yield, bugs, disease etc., happens because I PLANT THE DANG CUPS, according to my wife. She, and others, say this is a definate no-no. I disagree. What do you say and why?

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