You can definitely convert all delta numbers to be positive (see below). However, as others said, it is somewhat unusual for treatment effects data. Perhaps, your advisor has some specific reasons for that recommendation - it is better to clarify this issue with the advisor.
Should you decide to follow your advisor's recommendation on that, you can perform conversion by choosing a different anchor point (baseline), which should make sense in the context of your study (if it does not, I would try to politely argue with this recommendation). However, in any case, you would still need to provide the rationale for that decision in your paper.
If your advisor's rationale for positive only percentage values is purely aesthetic, then there is an easy solution to this "problem", especially since you're asking about table format. Just add an "Effect" (or similarly named) column to the table. For original negative delta values, simply indicate that by placing word "Decrease" (or "Negative") into the corresponding cell, while placing the absolute value of the delta into the corresponding column. The effect in the results can also be indicated in writeup, such as "... increased by five percent" and "... decreased by seven percent".