Yes. Pretty Links Pro includes a native control for keeping specific keywords out of replacement.
Excluding Keywords
Go to Dashboard > Pretty Links > Options > Replacements and find the Ignore these keywords field.
Enter each word or phrase you never want auto-linked, then save. Pretty Links skips every term on this list when it scans your content for keyword replacements.
This helps when a keyword you replace elsewhere also appears where you want it left alone — brand names in quotations or headings, for example.