That connection does look frightening. Some good resources for finding safe routes are:
(This guy has collected pretty much all of the bike routes in portland and surrounding areas. Click at the bottom of the map to see more southern areas, including River Road. There's also some information about getting from Milwaukie to Portland if you click on Milwaukie on the bottom right list.)
maps.google.com is a good resources, if you click on the satellite button at the top right, to get a look at the roads (and to some extent, the level of traffic). I've used this numerous times when I've been interested in a route, but didn't feel like going out and driving it. However, sometimes it's difficult to see bike lanes when trees are in the way, so it's not perfect. But overall I think it's a helpful tool.
Another good resource, if you're concerned about mileage and elevation gain, is gmap-pedometer. You can trace your routes and it will give you the mileage, and you can look at a graph of the elevation. This doesn't solve your current problem, but it could prove useful.
As for specifics, it seems that River Road to 99E to 17th is your best bet, unless you want to go way out of your way. I think you should either drive it in your car, thinking about what it would be like if there were a cyclist on the road ahead of you, or else take a test run on a day you don't work, and just be very careful. If it gets too frightening, you can either walk your bike on the side walk or turn around. From the map, it looks a little hair-raising, but doable. And I think as you get used to the traffic, you'll learn how to better be aware and prepared.
After that bit, I respectfully disagree with Steck. You should also consider turning right on Bybee, going past Reed College along Woodstock Blvd, and turning left on 41st. It's a nice bike route with a bike lane, that takes you north on 41st, 42nd, and 43rd, depending on where you are. Crossing Powell is a rough spot, but you get a light and I don't find it to be too bad. Also, remembering the route can be tricky, but now it's marked so you know which of the streets you are supposed to be on. The reason I recommend this route over the Springwater Corridor is that it's more direct and it avoids you having to bike on Hawthorne from the river to 45th. That sounds frightening to me. I don't even feel comfortable driving in my car from about Ladd's Addition to 39th Ave. I've just seen too many scary drivers and conjestion along there. I think you should try both Springwater Corridor and Hawthorne (or more likely, as steck suggests, a side street) as well as the 41st route, and see what you like better.
I personally have a few different routes I use to get to work, depending on what challenges I want to deal with (long, mild hills or shorter very steep hills; pedestrians along a multi-use trail or traffic along streets). I also find that when I get sick of a certain route, it's nice to have another one, to spice things up a bit.
Also, if you're having problems with motivation, build up slowly. Say, I'm going to bike in once a week for a couple of weeks, then twice a week, then three times, etc. And also, be glad you don't work on top of Marquam Hill. Talk about making excuses, that hill is an easy excuse not to bike to work.
So check out the River Road to 99E to 17th connection either by bike or by car, and try out the Springwater route and the 41st route, and let us know what you find.