Here's a couple options. Don't worry too much about which option you choose, either one will work OK.
Most Wye transformer secondaries would have a secondary voltage of 120/208. Running a 240-volt heater at 208 is OK, but beware that your output will be (208/240)^2 = 75% of rated -- that might or might not be a problem for you, you might or might not need to provide additional heaters or bigger heaters. Maybe you can get heaters rated at 208 rather than 240. This is a very common configuration, that alone might be a good reason to choose it.
Another option for you might be a 120/240-volt center-tapped delta. That would give you 3-phse 240, plus it would give you some 120-volt control voltage. Beware that you can only derive 120 on two out of the three legs; the third leg can be used only for 240-volt 2-pole or 3-pole loads, NOT 120-volt. This is kind of an unusual animal, you might want to avoid it for that reason, but otherwise it seems to lend itself well to your application.
Regardless of the secondary configuration, NEC 250.20(B) REQUIRES that it be a grounded system; ungrounded is NOT an option.
Regarding safety: well, the maximum voltage to ground on a 120/208-volt wye is 120; max line to line is 208. The maximum voltage to ground on a 120/240-volt center-tapped delta is 208; max line to line is 240. So, there's a slightly higher voltage to deal with on the 120/240, but it's not a tremendous difference. It's a moot point if you're used to 277/480-volt systems, which you probably are since I'm guessing that's your transformer primary voltage. Both systems will impose a voltage on both heater terminals, no way around that.
NOTE: you might want to double-check if your heaters have any maximum listed voltage to ground -- if there's a stated maximum of 120, then you CANNOT use the 120/240-volt center-tapped delta. You could, instead, use three single-phase 120/240-volt transformers, but I can't think of any good reason why you'd want to do that.
Regarding proper grounding method: Well, you need to bond the neutral of either system to ground in accordance with 250.30, the requirements there are pretty clear. The requirements are about the same as for any transformer or service entrance installation.
Hope this helps.