This can be argued both ways. There is a way to say that whistleblowing does violate company loyalty and there is a way to say that it does not.
On the one hand, blowing the whistle would certainly seem to violate company loyalty. When you blow the whistle, you are harming the company. If you owe loyalty to a company, it is certainly not loyal to harm that company. Since you work for the company and the company has given you a way to support yourself, you do owe it loyalty. This does not mean that you cannot be a whistleblower. However, it means that you must have a duty to blow the whistle that is strong enough to overcome the wrong that you are doing to the company.
On the other hand, you can argue that this is not a violation of loyalty. There are at least two ways to make this argument. First, you can say that the company is actually harmed if you do not blow the whistle. The company will be harmed if it acts in ways that are unethical and immoral. In the long run, it will likely be exposed and hurt. Therefore, blowing the whistle prevents the firm from digging itself deeper into this hole. Second, you can say that you really do not owe a company much loyalty. The company would surely fire you if it felt you were acting wrongly. You and the company are not pledged to one another in all circumstances. You are in a marriage of convenience that does not include the expectation of loyalty.