She's entitled to half the change in value of the pension from date of marriage to date of separation. Your pension administrator can easily calculate this for you if you ask. They do it a lot.
Now, you have an asset value you can include in your equalization process. If she has a pension from her job, that goes in the mix too. You can divide up the assets however you like. Maybe your pensions are pretty similar and it's a wash. Maybe you get to keep your whole pension but she gets her own pension plus more of the value of the house. (But keep in mind you need a place to live and your pension is not nearly as liquid an asset as your share of the house.) If you give her the entire share of the pension, it will go into her own pension if there is a transfer agreement, or into a locked-in RRSP she can't access until her own retirement. Your pension income would drop in that scenario as you are now drawing from a smaller asset.
Be cautious - for a federal pension, the pension administrator is really a stickler for fairness. Even if you come to a legal agreement that she lets you keep your pension (maybe she expects a big inheritance and is being kind or something), she can change her mind later. Unless you can prove in your separation agreement that she got another asset of appropriate value, if she approaches them and says "look, equalization of pension wasn't done properly" they WILL give her share to her.