First, most recommendations about frequency of eating and timing of eating don't have any appreciable real benefit. Whether you get all your daily nutrition in 3 meals or 6 only matters in what helps you stick to your nutrition plan. If you do better eating small meals throughout the day, do it. If you do better with multiple larger meals, go for it. Long story short:
Any recommendation of not eating at least N hours before bed is suspect.
The only place I've seen something different is when we are talking about a good insulin spike. It takes about 7 hours for your body to switch from burning carbs to burning fat. If you are concerned with burning as much fat as possible, be concerned if your last meal contains carbs. Since you are talking about having a protein shake before bed, the insulin response is not enough to cause your body to completely switch over where it's pulling it's energy. If you are happy with your body composition, there is nothing to worry about at all--except that you have to keep in mind that protein shakes also have calories.
Studies showing the efficacy of protein have mixed results.
What this means in lay terms is that it doesn't matter as much when you consume the protein as the amount you consume. While it has been proven that your body can only process protein so fast, and exercise prepares your muscles to use the protein in your diet, it hasn't been proven you have to consume the protein just after you eat. If you have your protein before exercise, it still takes time to process, and it will be present when your body is ready for it.
Long story short: it doesn't matter which you choose. If your stomach gets upset consuming it post workout, try it pre-workout. Either way it will still do what it needs to.