I've had similar musings about transit re-use. The most parsimonious rail connection would indeed be an elevated structure above Memorial Blvd (makes sense, as that's what it was designed for), and you could conceivably build a modern and attractive minimal viaduct that eventually descends under I-95 to reconnect to the NEC. This bypasses the new Amtrak station of course, but could be served by Kennedy Plaza and reclaiming part of the old Union Station property.
If you wanted to link to the new station itself, you could maybe have light rail come over an elevated structure across N. Main, over the currently-undeveloped property South of EDGE College Hill and Canal St, weave past One Citizens Plaza to the left or right, and descend to the parking lot near Moshassuck Ct to a culvert under the Avalon, connecting to the ground floor of the station parking garage - this COULD tie into the NEC but the grade change and turns might be a bit tough for current rail stock, so you could perhaps convert the bottom of the garage into a new light rail station connection, leading to the West and South of Providence.
The other possible solution is BRT use, if you redevelop the parking lot between the tunnel portal and N. Main into a ramp down. Of course, all of these options require the
bascule bridge to the East to be in the lowered position, and also not a park/art piece.