I can't speak to anyone's specific plans, but....

Our travel agent tells us that the Chunnel is trains-only,

Other trains use the Eurotunnel/Chunnel including car-carrying shuttle trains. Your agent may have formed an opinion based on what they are able to book.

... Is there a ferry, and if so, what are the departure and arrival points?

This booking site has a nice drop-down list of ferry routes... No idea about their other qualities as I've never used them. I *do* vote for a nice slow ferry crossing at least once. Summer time, shouldn't be too rocky, not really that slow (1.5 hours Dover Calais, IIRC)

If we're all by ourselves, we'd like to avoid France if possible. I don't savor the idea of changing trains in France after going through the Chunnel. But if we were traveling with someone who's done it before, then it wouldn't be a problem.

Trying to avoid the occasional French strike, are we?? Well, FWIW, you could get to Amersfoort from London by train without putting your foot on French soil, but you'd still have to see a small bit of French territory. You can get a Eurostar from London/Waterloo to Brussels, then change to the Thalys to Amsterdam/Schilpol, then change to Amersfoort.

The Bahn's schedule site will let you look at your options (but won't give pricing for many cross-system bookings).

From a cost perspective, you are in a tougher spot since British Rail isn't an option in many (all?) of the multi-country rail passes, so the idea of getting a 3-country "select" pass is less useful if your itinerary plan is UK/Netherlands/Germany.

My memory is that Eurostar tickets were extra-expensive when I booked them on day of departure, and, if your schedule firms up, you might save a bit by booking before you leave. If your agent doesn't seem up to speed on rail ticketing, I can say that I gave had decent experience with Rail Europe over the phone for complicated tickets. The Rick Steves site also showed some sorts of sales omnpasses, so you might take a gander there.

Do I take it you might think about getting a car and driving from England? (just wondering about dragging a RHD car around in LHD countries and whether an agency would even let you drop it without charging big bucks...)