Definately have her see a doctor!!!! I also have severe pain during intercourse. It's a condition called dyspareunia (i am not sure about that spelling) there are many things that could be causing it. I personally have been to several doctors over the past year, and we are still ruling things out. She should set up an appointment with her gyn asap. They can give her suggestions for easing the pain until they can get to the bottom of it. Make sure she goes prepared though, I was rather caught off gaurd with some of the questions they asked. They may ask personal questions such as exactly where the pain is, what part of intercourse causes the pain, how deep is penetration when the pain begins, can she describe the pain, etc.

sometimes the questions seem embarassing, but they are important. Have her google or web search dyspareunia. Maybe she can find symptoms like hers or close to hers, so she can take it to the doctor and say "this is what i'm feeling." unfortunately, there are a lot of doctors who do not know the reasons for dyspareunia, so her doing some research herself may help the doctor understand what she is feeling. They will also do a physical exam.
Because your wife is pregnant, I am not sure what they can do for her. My doctors have tried a few different antibiotics, birth control (the hormones are supposed to help) and over the counter pain killers. I am also going to counseling to help me cope with the psychological damage the pain has caused (even the thought of sex gives me pains now) and my husband is coming with me next week. Painful intercourse can have emotional effects for both of you. Make sure any lubricant you use with her is water soluable, and have her urinate and wash with luke-warm water after intercourse. She shouldn't take bubble baths, as that makes the area more sensitive and prone to infection.
My pain still occurs, so I can't give any real surefire "this is what I did and the problem went away" solutions. I hope what i've told you has helped, and good luck!