This answer (to a different tiling problem) gave me the idea to use more than 2 colors to color the 7x9 rectangle (I have already tried the chessboard coloring without any success).
I devised a coloring scheme with which every 2x2 square always covers the same number of fields for each color, independently of its position. This can be achieved using 3 colors (say, a, b and c):
ababababa
bcbcbcbcb
ababababa
bcbcbcbcb
ababababa
bcbcbcbcb
ababababa
The number of fields per color: $a = 20, b = 31, c = 12$.
Every 2x2 square covers 1 a-, 2 b- and 1 c-fields. Let $S$ denote the total number of 2x2 squares.
There are 3 groups of L-shaped trominos:
- Group-1 trominos cover 1
a-, 1 b- and 1 c-fields.
- Group-2 trominos cover 1
a-, 2 b- and 0 c-fields.
- Group-3 trominos cover 0
a-, 2 b- and 1 c-fields.
Let $L$, $L_1$, $L_2$ and $L_3$ denote the total number of L-trominos, and the number of trominos in each group, respectively. The following equations hold:
\begin{align}
L_1 + L_2 & = a - S \\
L_1 + 2L_2 + 2L_3 & = b - 2S \\
L_1 + L_3 & = c - S
\end{align}
(Note: The summation of these equations gives
\begin{align}
3(L_1 + L_2 + L_3) & = a + b + c - 4S \\
3L + 4S & = a + b + c \\
3L + 4S & = 63 \; (= 7 \cdot 9)
\end{align}
as expected.)
The solution for the above system of equations:
\begin{align}
L_1 & = \frac{2a - b + 2c - 2S}{3} = 11 - \frac{2S}{3} \\
L_2 & = \frac{a + b - 2c - S}{3} = 9 - \frac{S}{3} \\
L_3 & = \frac{-2a + b + c - S}{3} = 1 - \frac{S}{3}
\end{align}
It's already mentioned in the question that the only possible values for $S$ are 0, 3, 6, 9, 12 and 15. Substituting these values into the expressions for $L_1$, $L_2$ and $L_3$ shows that while both $L_1$ and $L_2$ are positive for all $S$ values, $L_3$ becomes negative for $S > 3$, which means that our tiling problem cannot be solved using more than 3 2x2 squares.