One way to fix this problem is with a shareholder's agreement that guarantees shareholders the right to participate in future funding rounds on a proportional basis to the shares they already hold.

So, assume you hold 99 shares and your employee holds 1 share. If you sell yourself 1B shares for $100, you'd be obligated to offer your employee ~10M shares (10101010, I calculate) for $1. If he accepts, your employee would continue to own 1% of the business.