I just wanted to add my two cents regarding what you said about your FW losing her extended family (and therefore her childhood), because I've been there.
My family all live in Canada or Poland, and my parents, brother, and I now all live in the US. My mom is a lot like your MIL, in a general sense. She has Borderline Personality Disorder, so the way in which she's toxic is a little different. Anyway, I cut her off and moved away to college when I turned 18. The only relative who would still talk to me was my grandmother, who had raised me until I was 10. When I was 21, my grandmother passed away. During my final visit to her (and the funeral a month later), I got to see my extended family for the first time in years. It was wonderful, and on the surface we got along just like old times! But my aunts and uncle (with whom I had been incredibly close) kept urging me to "make up" with my mom. They had believed all of her lies. So I tried to "make up" with my mother, and after three years of no-contact, things went well for a time.
At the time, I had just begun a relationship with the man who is now my husband. He waved at my mom across a driveway once. Luckily, that's all he's ever seen of her (or anyone in my family). She knew we were getting serious, but my mom doesn't even know his (now our) surname. Why? Because she started making threats to call CPS and tell them "whatever she had to" in order to take my kids away if I ever had any. And I don't doubt for a second that she would create huge problems for us. I unfortunately cannot trust my extended family not to tell my mom my married surname, my address, or to tell my mom when a grandkid is born. As a result, I cannot have contact with them at all. It really sucks, but a person that crazy and vindictive will use whatever means necessary (even exploiting extended family) to get to you, and if you ever want to have kids, that could be a HUGE issue. It still hurts a lot (it's been nearly five years now), but I don't regret it for a second. When we have a child, I'll be even more sure. I may have lost my childhood, but my own child's will be all the more secure for it without a scary, horrible "grandma" to harm them. I look at old photos often, and even do genealogy as a hobby, because it makes me feel closer to the family I once had. I think of them fondly quite often, and my child will be well aware of his/her heritage. We may even travel to Canada or Poland together, without visiting any relatives. Likewise, if she ever feels up to it, your FW can still visit Slovakia, see the sights and eat at the restaurants, with just the family you two have made. It's not the same, but it's something. I'm looking forward to showing my husband my hometown; we won't see my relatives, but he'll get to see the city and my school and the park I played in, visit my favourite attractions and eat the local food.
Thankfully, my husband's family has been more than welcoming. My MIL is her own special type of crazy, but she's loving and warm and makes me feel wanted. I lost a brother, but gained a sister in my SIL. They're far from perfect, but they're KIND. Perhaps getting your wife as involved as possible with your family, asking your parents to be there for her in place of her own, might help ease the transition. My MIL and I have grown incredibly close over the past 5 years, and I don't know how I would have coped without her. Since your mom is already well aware of your MIL's craziness, perhaps she can forge a strong, maternal bond with your FW, if they haven't already. If we hadn't eloped, I would have gladly had my FIL or GFIL walk me down the aisle. Your FW might be losing a family, but in marrying you, she's gaining another one...as well as making a brand new one with you! And you sound wonderfully supportive, so I'm sure the two of you will come out on top.